A double-layer shutter control method of a multi-sputtering system provided with three targets in a single chamber and a double-layer rotating shutter mechanism having shutter plates which independently rotate and have holes formed therein, comprising selecting a target by a combination of holes of a first shutter plate and a second shutter plate and uses the selected target for a pre-sputtering step and a main sputtering step with continuous discharge so as to deposit a film on a substrate, whereby it is possible to prevent cross-contamination between targets due to target substances etc. deposited on the shutter plates.