A substrate processing apparatus, which utilizes a first transfer apparatus and a second transfer apparatus which are configured to transfer a transfer container containing a plurality of substrates, along a first transfer path and a second transfer path whose lateral positions differ from each other, respectively, including a first load port where the transfer container is loaded and unloaded by the first transfer apparatus, and a second load port that is arranged stepwise with respect to the first load port, with the transfer container being loaded to and unloaded from the second load port by the second transfer apparatus.