A substrate processing apparatus 1, which utilizes a first transfer apparatus 104A and a second transfer apparatus 104B which are configured to transfer a transfer container 10 containing a plurality of substrates, along a first transfer path 102A and a second transfer path 102B whose lateral positions differ from each other, respectively, comprises a first load port 21 where the transfer container 10 is loaded and unloaded by the first transfer apparatus 104A, and a second load port 22 that is arranged stepwise with respect to the first load port 21, the transfer container 10 being loaded to and unloaded from the second load port 22 by the second transfer apparatus 104B.