Provided is a substrate processing apparatus including: a substrate processing unit configured to accommodate a substrate in a processing chamber, and process the substrate; and a control unit including a storage unit, a main storage unit, and a user interface unit. The control unit includes: recipe optimizing means configured to calculate a difference between measurement data obtained by measuring a processing result of the substrate and a target value, and optimize a recipe by changing some of processing conditions of the recipe so that the difference becomes smaller, and recipe batch-optimizing means configured to retrieve a batch-optimizable recipe in the storage unit in connection with the recipe and change some of processing conditions on the retrieved recipe like the recipe, on which the optimization is being performed.