The present invention proposes an in-situ freezing machining method for an integrated thin-walled array structure. In the method, the area among cups is cut off first; then, the outer walls of a cup array are machined; and finally, water filling and freezing are carried out, and in-situ freezing machining of the inner walls of the cup array is carried out. Then, hoisting and turning over are carried out, and the area among cavities is cut off; then, the outer walls of a cavity array are machined; and finally, water filling and freezing are carried out, and in-situ freezing machining of the inner walls of the cavity array is carried out. The method realizes in-situ freezing clamping of workpieces, avoids error accumulation caused by repeated installation of a fixture, and can refrigerate efficiently, suppress ambient and cutting thermal interference, and ensure the stability of freezing fixture.