This Ocarina of Time 3D Boss Guide covers every boss in the game in order. It does not cover the mini-bosses.
Ocarina of Time 3D Boss Guide
*Note* this guide is currently being updated for the 3DS version of the game
Gohma
Tap the VIEW button on the touchscreen and look around until you see Gohma. It will fall down. Simply L-target it and when the eye turns red, shoot it with the slingshot. This will stun the creature. Hit its eye with you sword over and over until it gets back up. Gohma will climb up to the ceiling, keep L-targeting it the entire time.
She will hang from the ceiling and the eye will turn red once more. Shoot it with the slingshot and she will fall down stunned. Simply attack her eye several more times with the sword. Repeat and before long, she will be defeated.
King Dodongo
L-target Dodongo and when he opens his mouth, toss a Bomb into it. This will stun the creature. Take out the sword and use a Jump Attack on it. It will start rolling, run the opposite direction and it will stop after hitting two walls. Repeat from the beginning and after 3 Jump Attacks, Dodongo is defeated.
Barinade
At the start of the fight, there will be a green, red, and blue tongue attached from the top of Barinade to the ceiling. L-target each one and use the boomerang to detach it. After detaching all three, Barinade will spawn jellyfish and start rotating them about the room. L-target Barinade's center and hit it with the boomerang, which stuns it. Jump Attack the center several times and it will come out of the ground and start moving about, while rotating jellyfish again.
Wait for it to stop and hit it with the boomerang. This will stun it and all of the jellyfish. Destroy all of the jellyfish, be cautious as it may become un-stunned during this process, and it will start spinning around the room unprotected.
While spinning around unprotected, hit it with the boomerang as it gets close. Jump Attack it several times and it will implant itself into the ground. Run around, dodging its attack's, and it will start moving again. Repeat a few times and it will be defeated.
Phantom Ganon
Start by standing on one of the Triforce symbols located about the room, which will allow you to not be harmed. Get out the Fairy Bow and look around at the pictures. Phantom Ganon will appear in two of them. One will turn around while the other leaps from the picture. Shoot the one as it come out of the picture, while it's white. I found it to be the one that is the brightest in color. Repeat 2 more times.
Phantom Ganon will now dismount and start hovering above you. L-target him and as hit throws a ball of energy at you, reflect it back with you sword. It will either miss, hit him, or he will reflect it back. If it hits him, he will become stunned. If he reflects it back, simply hit it with the sword again. Attack him with the sword a couple times. He will start hovering again eventually, just repeat a couple times and he will be defeated.
Volvagia
Run into the center of the room and it will appear. When the fight starts, it will be located inside of the lava spots on the ground. There will be some lava spew from one of them; this is the one it is going to appear from. Dodge its initial attacks and then attack the head with the Megaton Hammer. This will stun him. Now Jump Attack his head, which will make him dive back into the lava pit. He will emerge from the lava pit and fly around the room, simply use the Fairy Bow to shoot his head a few times and Volvagia will dive back into a pit. Repeat several times and he will be defeated.
Morpha
Run into the center of the room and it will appear. The nucleus, a reddish ball, will be moving about the room. The key to this fight is to Longshot it and attack it with the sword. Periodically, water arms will form, stay away from them, and the nucleus will get sucked into them. This is the easiest time to longshot it. After hitting the nucleus several times, Morpha will vanish defeated.
Bongo Bongo
Unless using the Lens of Truth, you will only be able to see his hands. First off, he will be pounding on the platform causing you to bounce much of the fight. You have to hit both of his hands, usually with the Longshot or Fairy Bow, and then he will charge you. Use the Lens of Truth and the main body will be visible, simply shoot it with the bow and it becomes stunned. Attack the eye with the sword several times. Repeat and after a few times, Bongo Bongo is defeated.
Twinrova
The fight begins with both sisters flying about the room. Jump onto one of the outlying platforms and wait until one of the sisters starts powering up for an attack. Lower the Mirror Shield, making sure to face the powering up sisters direction, and when she attacks, the beam will be reflected. Use the circle-pad to direct the beam towards the opposite sister. Repeat several times and they will join, becoming a single enemy.
Jump from the platform into the center of the room. L-target Twinrova and lower the Mirror Shield. She will launch each a fire or ice attack at you. As long as you have the Mirror Shield out, the attack is absorbed. Simply absorb three of the same type attacks, making sure not to absorb two different types or else you will get hurt, and the mirror shield will start emitting a beam. Direct the beam towards Twinrova to stun her. Run to her and attack with the sword several times. She will become un-stunned rather quickly. Repeat several times and she is defeated.
Ganondorf
This man is the first part of the final boss battle of OoT. For this fight be sure to have green potions (blue potions are better for this battle) and many arrows! Ganondorf only has two modes of attack, a magic ball attack similar to that of Phantom Ganon's and a giant black collection of energy. To harm Ganondorf when he launches one of the magic ball attacks launch it back at him using your sword (similar to Phantom Ganon but this time Navi is unable to allow you to use Z-targeting) and keep up the volley until he slips up and gets hit by it. Now while he is stunned from the attack hit him with a light arrow to cause him to fall to the floor and have to recover. Leap over to him and let loose with vicious attacks (remember the JUMP ATTACK!! It still does double damage this far in the game!) Eventually he will begin using his second attack a larger collection of energy. When he starts collecting energy for the attack hit him with a light arrow and attack him while he is down. Repeat until defeated!
Ganon
Now this is it you've come a long way from being the boy without a fairy in Kokiri Forest! And speaking of fairy Navi has returned to aid you (that means Z-targeting is back!) Ganon is a large boss with dual-swords this will be your greatest struggle yet!! When the fight actually begins The Master sword is launched outside the ring of battle as well as Zelda. But you can still harm the giant. Back away and use a light arrow to hit him in the face and stun him, now run around behind him and use the Biggoran's Sword or the Megaton to hit his tail (his weakpoint) and if you don't have any light arrows you can use your Longshot but you'll have to move much faster since he does not stay stunned as long. After he takes a large amount of damage Ganon will attacks will become faster and more powerful. But on a more positive note Link will have the Master Sword back! So now the playing field has been leveled and you're truly ready to defeat the King of Darkness! Hit him in the face with more light arrows (or your Longshot) and stun him and attack him. After you damage him enough Ganon will be down and out and Zelda and the other six sages will seal the King of Darkness away for good!
