Phase 1: Crushing the Thwomp
Head Thwomp is a large, stone block boss that moves up and down, attempting to crush Link. The boss room has four holes, one in each corner. Your objective is to lure Head Thwomp over one of these holes. Equip your Roc's Feather. When Head Thwomp is directly above a hole and begins to descend, use the Roc's Feather to jump into the hole yourself.
If timed correctly, Head Thwomp will fall into the hole, flipping over and revealing its vulnerable underside. Quickly exit the hole and attack its underside with your Wooden Sword. Head Thwomp will then right itself and resume its crushing pattern. It may also occasionally spawn small enemies or projectiles, so be ready to dodge.
Phase 2: Repeating the Process
There isn't a distinct second phase, but rather a repetition of the first. Continue to lure Head Thwomp over a hole, jump into the hole with the Roc's Feather, and then attack its vulnerable underside with your sword. The timing can be tricky, so observe its movement pattern carefully. Don't get greedy with your attacks; one or two hits and then prepare for the next cycle.
After enough hits, Head Thwomp will be defeated. You will be rewarded with a Heart Container and the Ancient Wood (Essence of Time).