Provided is a substrate processing apparatus, which comprises a process chamber configured to process a substrate, a first plasma generation chamber in the process chamber, a first reactive gas supply unit configured to supply first reactive gas into the first plasma generation chamber, a pair of first discharge electrodes configured to generate plasma and to excite the first reactive gas, a first gas ejection port installed in a side wall of the first plasma generation chamber to eject an active species toward the substrate, a second plasma generation chamber in the process chamber, a second reactive gas supply unit configured to supply second reactive gas into the second plasma generation chamber, a pair of second discharge electrodes configured to generate plasma and to excite the second reactive gas, and a second gas ejection port installed in a side wall of the second plasma generation chamber to eject an active species.