A substrate processing apparatus includes: a chamber; a substrate support disposed in the chamber; a plasma generator configured to form a plasma in the chamber; and a controller configured to perform a process including: placing a substrate on the substrate support, the substrate including a first film, a second film and a third film, the first film containing a silicon, the second film having a second aperture, the first film being disposed between the second film and the third film; cooling the substrate to −30° C. or less; etching the first film through the second aperture with a plasma formed from a first process gas containing a fluorocarbon gas, to form a first aperture of a tapered shape in the first film such that a width of the first aperture gradually decreases toward a bottom of the first aperture; and etching the third film through the first aperture.