Step 3. Microwave the salmon on high for about 1 1/2 minutes, depending on the thickness of the fish. Flip the salmon and cook for another 1 1/2 minutes.The salmon is done when it is just beginning to flake.tep 3. Microwave the salmon on high for about 1 1/2 minutes, depending on the thickness of the fish. Flip the salmon and cook for another 1 1/2 minutes.