The invention discloses a three-dimensional reconstruction system calibration method based on multi-frequency structured light. The calibration method comprises the following steps of step S1, initializing equipment; step S2, preparing a calibration board; step S3, acquiring a calibration image; step S4, calibrating a camera; step S41, determining kp0; step S42, determining kp1 and kp2; step S43,determining kp3 and kp4; step S44, searching the remaining of small circles; step S5, calibrating a projector; step S51, generating a G matrix by using a calibration board white-light chart; step S52,unwrapping phase; step S521, acquiring a grating projection chart; step S522, unwrapping the phase; step S523, iteratively computing to obtain the finest stripe absolute phase; step S53, solving parameter; and step S6, ending. The calibration method provided by the invention has the advantages of being simple in calibration process, high in accuracy, strong in practicability, convenient to use and low in cost.