In order to break through the restriction of application scene caused by the limitation of single wavelength of conventional laser projector and realize the layer projection of different parts, different materials and different assembly processes, a multi-color layer laser scanning and auto-focus projection system was designed and established. Two wavelengths of laser were adopted as the light source, and according to the different positions of dichromatic mirror, the two laser scanning and auto-focus projection schemes of multi-color co-optical axis and separate optical paths were proposed, and the corresponding mathematical models of optical system were deduced. By adjusting the distance between mirror groups through the auto-focus function of the system, the minimum light spots of different colors could be focused on the projectors at different distances. Two kinds of projection optical systems were simulated by ZEMAX optical design software, and the reliability and projection effect of the two systems were compared and analyzed. The experimental results show that on the projection plane at 3 m, the spot diameter of various wavelengths of the co-optical axis system is within 0.8 mm and the spot size is uniform, which can achieve the scanning and auto-focus projection function of multi-color layers.