A calibration method of three-dimensional measurement system includes a projection device, a camera and a processor. The projection device projects structural light to a reference object including a first calibration surface and a second calibration surface. The camera photographs the reference object to obtain at least one reference object image. The processor performs decoding according to the at least one reference object image to obtain a plurality of pieces of phase data of the at least one reference object image. The processor computes a first phase corresponding to the first calibration surface and a second phase corresponding to the second calibration surface according to the phase data, calculates a surface phase difference between the first phase and the second phase, and computes according to the surface phase difference and a height of the second calibration surface relative to the first calibration surface to obtain a phase-height conversion parameter.