Abstract: A substrate processing system includes: a substrate processing apparatus including a stage on which a substrate and an annular member are placed; a substrate transport mechanism including a substrate holder; a distance sensor provided in the substrate holder; and a control device, wherein the substrate transport mechanism is configured to place a jig substrate having a reference surface as a reference for a height of the annular member on the stage, wherein the distance sensor is configured to measure a distance from the substrate holder positioned above the stage to the reference surface of the jig substrate and a distance from the substrate holder to the annular member, and wherein the control device is configured to estimate the height of the annular member based on a measurement result of the distance to the reference surface and a measurement result of the distance to the annular member.