Stick to the low ground and fire charged beam shots directly at the SA-X to destroy it. Your beam must be fully charged to damage it. As it approaches, Space Jump over the SA-X to the other side of the floor while charging your beam, and release the shot when you land.

Only the Charge Beam and Screw Attack can damage the SA-X, though Ice Missiles can temporarily immobilize it. The Screw Attack is also ineffective, as Samus will take damage as well, even while the SA-X is frozen. The SA-X has a tendency to use its own Screw Attack as a counter-attack whenever Samus lands a blow.

For unexplained reasons, the Omega Metroid from Metroid Fusion attacked Samus despite the latter having Metroid DNA, whereas the other Metroids in the Restricted Area ignored her. This may be because the Metroids in the Restricted Area were preoccupied with the SA-X who admittedly was attacking them at the time.

At first you won't be able to injure this huge creature with any weapon in your arsenal, even Ice Missiles won't have any effect. Instead, wait for the Omega Metroid to slash out and strike Samus deliberately, you'll then lose all your health except for 1 unit of energy.