A substrate processing control method in a substrate processing apparatus, includes: acquiring a data set for each substrate sequentially subjected to first and second processes at first and second levels, the data set including information specifying the first level at which the first process has been performed, information specifying the second level at which the second process has been performed and information about a characteristic amount relating to characteristics of the substrate; calculating information including an expected value of the characteristic amount, and level deviations of the first and second levels to the expected value based on the data set; and correcting the first parameter at the first level or the second parameter at the second level based on the calculated information.