Based on femtosecond laser scanning interference, this paper dedicated to the surface profile measurement of silicon wafers. Femtosecond laser has not only low time coherence, but also high spatial coherence and high measurement accuracy. This measurement system is on the basis of a Michelson interferometer. Stepping motor is used to move the measuring arm so as to scan the surface of the measuring object. Then, the reconstruction of the object’s surface profile is accomplished by the algorithm. We use a short-wave infrared camera to record the interference fringes. The surface profile is reconstructed with pixel points, so the pixel size of the camera is the key to the reconstruction. In this paper, a standard part is selected and measured, then the camera pixel is calibrated through the size of the standard part. In this paper, the grating is tested as a standard part, and the camera pixel is calibrated through the grating reticle. Finally, the surface profile of the silicon wafer was measured with the calibrated system.