The invention provides a substrate processing apparatus capable of removing unnecessary deposition films attached to a bevel portion of a substrate to be processed with high efficiency and at low cost without causing damage to the inner areas of the substrate to be processed having patterns formed thereto and without causing heavy metal contamination. The substrate processing apparatus comprises a rotary stage 1 on which a substrate 2 to be processed is placed having a smaller diameter than the diameter of the substrate 2, a gas supply structure unit 3 disposed above the substrate 2 to be processed for forming a gas flow for protecting a pattern formed on an upper surface of the substrate to be processed, a first gas supply system 11 for supplying nonreactive gas to the gas supply structure unit 3, an atmospheric pressure microplasma source 4 having a nozzle for supplying radicals for removing unnecessary deposits on an outer circumference portion of the substrate to be processed, a second gas supply system 14 for supplying gas to the atmospheric pressure microplasma source 4, a high frequency power supply 13 for supplying power to the atmospheric pressure microplasma source 4, and a vacuum means 5 for vacuuming and removing reaction products from the outer circumference portion of the substrate 2 to be processed.