The matching link of the three-dimensional (3D) measurement system based on the dual line-scan camera is easily affected by the surface texture and light source, affecting the point cloud’s accuracy and integrity. This study investigates a grayscale matching algorithm based on Fourier transform to achieve high-precision matching and deal with partial overexposure. Additionally, the imaging model of the measurement system is established and a flexible static calibration method for line-scan cameras is introduced. Finally, an experimental platform is developed to verify the proposed matching algorithm’s effectiveness and the measurement system’s accuracy. The reprojection error of the camera calibration results is better than 0.3 pixel. Based on the proposed algorithm, the measurement point cloud is complete and can reflect the real shape of the depth mutation of the object. The root mean square error of standard plate from the point cloud to the fitting plane is 0.023 mm. Results show that proposed matching algorithm can effectively ensure the integrity of the point cloud and retain the surface details of the measured object.