A substrate transfer apparatus, for transferring a substrate from a first module to a second module, includes a moving base having a Y-motion axis for moving the moving base in Y-direction, and a substrate holding member mounted to the moving base via X-motion axis so as to move relative to the moving base to be in an advanced position and a retracted position relative to the moving base. The X-motion axis operates when the Y-motion axis is operating, if the X-motion axis must be parallel to the Y-motion axis when transferring the substrate from the substrate holding member to the second module.