A substrate processing method includes: (a) carrying a substrate having a first film with a recess, and a mask into a first chamber; (b) adjusting the substrate temperature to 200° C. or higher; (c-1) supplying silicon-containing reactive species into the first chamber, thereby adsorbing the species onto the side wall of the recess; and (c-2) supplying nitrogen-containing reactive species into the first chamber, thereby forming a second film on the side wall of the recess; (d) carrying the substrate into a second chamber; and (e) adjusting the substrate temperature to 100° C. or lower; and (f) etching the bottom of the recess. Further, (a) to (f) are repeated in this order until an aspect ratio of a depth dimension from the opening of the mask to the bottom of the recess becomes 50 or more.