The Crab Puncher attacks by punching with its giant claws, while some platforms with damaging but non-lethal spikes head towards it and destroy on contact with him. The lower claw is avoided by standing on a low platform and then jumping to a higher one, and the higher one is avoided by standing on a high platform and then falling to the floor. It also attacks by shooting bubbles, with some of them trying to home onto Mega Man (they can be identified by a yellow sphere inside them). The player will know the Crab Puncher is going to do this because he will protect his eyes with its claws. They are avoided by running at the left and then rapidly run towards the Crab Puncher when the homing bubble approaches Mega Man.
The Crab Puncher's eyes are its weak points, and each eye is half of the boss' health (fourteen HP each eye). The claws, although optional can be destroyed (each having twenty HP), making the fight easier. However, they are invulnerable if they are blocking its eyes.
- For the former, it should be fired above the eyes so that the lightning hits both eyes at once. However, if the cloud hits an eye, it will be destroyed and do minimal damage. Skilled players can defeat the Crab Puncher in just one use of this weapon.
- For the latter, firing it right in the middle of the boss' face will cause the explosion to hit both eyes for massive damage, hitting each eye twice. Again, if the missile hits an eye directly, the Commando Bomb will only do minimal damage.
The best weapon to use against the pincers is the Triple Blade; at close range, it will deal massive damage to each as two blades will hit their target, allowing the weapon to make short use of each pincer with ten blades. It should be paired with any of the Crab Puncher's weaknesses above.
On Easy Mode, the crab will be farther than normal, and it will shoot less bubbles. On Hard Mode, the crab will be nearer than normal, it shoots more bubbles, and it will move its eyes around at different angles. This gives the player less room and time to react, and makes it harder to hit the boss' eyes.
- Crab Puncher slightly resembles Gazamir, a sub-boss from Phoenix Magnion's stage in Mega Man Zero 2.