Substrate transfer method and substrate transfer system

A method includes: receiving a substrate on a first stage by a holder of a substrate transfer mechanism; causing the substrate to pass through a first measurement part, and measuring a first true deviation amount between the holder and the substrate at a first position; causing, when transferring the substrate toward a second stage, the substrate to pass through a second measurement part, and measuring a second true deviation amount between the holder and the substrate at a second position; reflecting a difference between the first and second true deviation amounts to a physical model to correct the physical model; calculating a position correction amount of the holder on the second stage from a thermal displacement amount of the holder at the second position; and controlling the substrate transfer mechanism based on the position correction amount to perform a position correction of the holder.