Multi-frequency-phase-shift structured light illumination scanning along two-direction will achieve higher robustness, but it increases time spending on scanning and computing. This paper proposes an improved coding and decoding strategy for scanning along two-direction by means of epipolar geometry. First, after scanning along vertical direction and getting unwrapped vertical phase, the temporary horizontal phase is obtained according to unwrapped vertical phase and epipolar geometry of system. Then, after scanning along vertical direction and getting wrapped horizontal phase, unwrapped horizontal phase is obtained by using temporary unwrap algorithm. Finally, a line-model is established between the camera and projector. When calculating a 3D point cloud, the intersection point of the camera line of sight and the projector line of sight is calculated, avoiding the traditional matrix inversion method and improving the point cloud calculation speed. The experimental results show that: 1) the root mean square error of final lateral phase is 4.89×10-3; 2) the computation speeds of 3D point cloud after scanning along two-direction and scanning along one-direction are improved by 6.08 times and 4.10 times, respectively; 3) the proposed 3D point cloud reconstruction method for scanning along one-direction is within the error range of 10-11 mm compared with the traditional method.