As current multi-spectral imaging system implements spectral separation and imaging by a filter wheel combined a common camera, it has larger volume, complex structure and is difficult to operate. To avoiding these shortcomings, this paper presents a novel design method for multi-spectral imaging system based on Micro-Electro-Mechanical Systems (MEMS). The method integrates a artificial-compound-eye structure and a multi-channel filter on one substrate to develop a compact multi-spectral imaging lens. The structure has several optical units, and each unit is used to capture the information for a certain band corresponding to red, green, blue, near-infrared bands. Based on this special artificial-compound-eye lens, a multi-spectral imaging system is setup. With this system, several contrast images aere acquired. The imaging experimental results demonstrate that the structure realizes color separation and multi-unit imaging as expected. Because of its high level of integration and ability of capturing the multi-band image, the novel artificial-compound-eye structure is suitable for smart multi-spectral imaging systems.