To provide a substrate processing apparatus which can perform flexibly various substrate processing, and to provide its method.

In flow recipe 39 and each flow recipe 40 including conveyance order of substrate, parameter of the treatment information of the substrate accompanies information which determines the conveyance order, and delivery of substrate is performed to a treatment portion based on the conveyance order. In a skip control flag which is one of parameter, treatment of the substrate is performed in a treatment portion in the flag when "ON" is set, and treatment of the substrate is not performed in the treatment in the flag when the flag is set as "OFF". Both of the treatment and the skip treatment can be operated by the skip control flag. Since the skip control flag accompanies the information which determines the conveyance order, whole of the flow recipe 39 and each flow recipe 40 whole are not necessary to be changed, and various substrate processing can be performed flexibly in accordance with setting of skip controlling flag.