Cragma will try to smash Link with his fists. While he prepares to do this, a glowing spot will appear on his body. Use the bow and arrow to shoot that spot.
Afterward, Cragma will slam both fists down, causing rocks to fall from the ceiling, including a big boulder. Stand near this boulder to make Cragma smash his fist on it, being sure to run out of the way at the last moment.
Cragma has flattened the boulder into a platform that you can pick up and carry around. Take the platform and put it onto the magma spout between you and the mine cart. Then use the platform to jump into the mine cart.
It will start moving automatically. As it spirals up the room, use your bow and arrow to shoot the shining spots on Cragma's body. If you miss one, Cragma might grab you and throw you down to the bottom.
After shooting the weak spots, you will reach Cragma's eye. Shoot it carefully (you need to be precise or the arrow will bounce off of Cragma's face instead) and then Cragma will fall. The mine cart will deposit you on the ground floor, where you should go hit Cragma's glowing head until he wakes up and starts smashing with his fists again.
Repeat the process as before, looking for arrows left behind by the falling boulders if you need more. Shoot Cragma's weak spots, make a platform with the fallen boulder, ride the mine cart up while shooting weak spots, hit Cragma's eye, then hit Cragma's head repeatedly until he dies.