Substrate processing control method, substrate processing apparatus and storage medium

The invention provides a substrate processing control method, a substrate processing apparatus, and a storage medium. Various parameters are properly controlled according to the state of substrate processing. A substrate processing control method in a substrate processing apparatus having a first element including a plurality of first level cells and a second element including a plurality of second level cells includes: an acquisition step, a data set acquisition unit that acquires, for each substrate, a data set including information specifying a first level cell on which the first process has been performed, information specifying a second level cell on which the second process has been performed, and information on a characteristic quantity of a characteristic of the substrate; a calculation step of calculating, based on the data set, information including an expected value of the feature quantity, a level cell deviation of the first level cell with respect to the expected value, and a level cell deviation