Shock waves occurring when opening a gate valve between two vacuum chambers and peeling of particles by a viscous force taking place when a gas is supplied into a vacuum chamber are necessary to be suppressed by the apparatus and method of the invention, whereby contamination of a substrate by particles is suppressed. If one vacuum chamber is a substrate processing chamber for performing a vacuum process on the substrate and the other chamber is a transfer chamber having a substrate transfer device therein, the gate valve is opened when inner pressures of both the vacuum chambers are less than 66.5 Pa and higher one thereof is less than twice a lower one thereof. Preferably, a purge gas for peeling of particles is supplied, before supplying the purge gas for pressure control, into the substrate processing chamber with a flow rate greater than that of the purge gas for pressure control.