A substrate processing apparatus includes a plurality of storage containers mounted on a load port, each storage container storing a plurality of substrates; a plurality of process chambers for accommodating the substrates; a transfer part for transferring the substrates; a memory for storing data tables, including first count data, for the process chambers; an operation part, when multiple substrates in the first storage container is transferred to the process chambers in a predetermined order and performs a predetermined process in the process chambers in a state in which no substrate is present in a first process chamber, counting first count data for the first process chamber; and a controller assigns flag data to a data table of a process chamber having largest first count data and when multiple substrates in the second storage container is transferred, control the transfer part based on the flag data from a different process chamber.