A substrate processing apparatus includes multiple first substrate processing devices, one or more second substrate processing devices and a transfer unit. Each of the multiple first substrate processing devices is configured to process a substrate one by one. The one or more second substrate processing devices are configured to simultaneously process multiple substrates, which are processed in the multiple first substrate processing devices. The transfer unit is configured to simultaneously carry the multiple substrates, which are processed in the multiple first substrate processing devices, into a same second substrate processing device.