The invention provides a substrate processing apparatus comprising a load port in which a transfer container containing a plurality of substrates can be placed, and a container storage part in which the transfer container can be stored, for performing various processes to the substrates which are drawn from the transfer container, the substrate processing apparatus being capable of increasing the number of times at which the transfer container is transferred to and from the load port, whereby the substrates can be processed with a high throughput. The substrate processing apparatus, 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).