There is provided a substrate processing method of a substrate processing apparatus. The substrate processing apparatus includes at least two targets, magnet-moving mechanisms disposed in one-to-one correspondence with the at least two targets, each of the magnet-moving mechanisms being configured to reciprocate a magnet in a first direction on a back surface of each target, and a substrate moving mechanism configured to move a substrate in a second direction orthogonal to the first direction. The method includes causing the magnet-moving mechanisms to reciprocate the magnets at different phases with each other.