A substrate processing apparatus that accommodates a substrate holder in which a substrate is placed in a processing container and forms a film onto the substrate, includes: a film thickness meter that measures a thickness of the film formed on the substrate; a state analysis unit that analyzes variation of the film thickness from a measurement result output from the film thickness meter at a plurality of measurement points where the film thickness on the substrate is measured; a singular point detection unit that, based on the analysis result, detects a measurement point where a difference from an adjacent measurement point deviates from a predetermined condition, as a singular point; and a singular point correction unit that corrects a measurement result of the singular point so that the difference of the film thickness between the singular point and the adjacent measurement point is within a predetermined condition.