A substrate processing apparatus includes a plurality of vacuum transfer modules including transfer mechanisms for transferring a substrate between a plurality of process modules arranged near the vacuum transfer modules that are configured to process the substrate under a reduced-pressure atmosphere; one or more load lock modules provided at each of the vacuum transfer modules; a first atmosphere transfer mechanism that transfers the substrate that is fed from outside to one load lock module; and a second atmosphere transfer mechanism that receives the substrate from the first atmosphere transfer mechanism and transfers the received substrate to another load lock module. The second atmosphere transfer mechanism is arranged above or below the vacuum transfer module that is provided with the one load lock module, and the vacuum transfer modules are arranged in series along a substrate transfer direction of the second atmosphere transfer mechanism.