A vision measurement system is placed in a protective cover made of a transparent medium to avoid environmental influences. Due to the deflection of light rays on the front and rear surfaces of the transparent medium, the imaging position of an object on the camera target plane is deviated, which makes the traditional vision detection methods based on the triangulation principle produce large measurement errors. This work introduces a three-dimensional (3D) reconstruction method by fringe projection system through a planar transparent medium. We derive the coordinate transformation relationship between a real-object point and a pseudo-object point caused by light refraction based on Snell’s law of flat refraction. Based on the relationship, a modified fringe projection method is proposed for unbiased 3D reconstruction. Two experiments, including 3D shape measurement of a white plate with ring markers and 3D shape measurement of a regular spherical object are conducted. The results demonstrate the effectiveness of the proposed method in such measurement environment.