In the biomedical field, to reduce the cost and dependence on advanced devices and to realize multi-dimensional image analysis for unlabeled samples, including spectra and structures, a multispectral microimaging system with multi-channel LEDs was independently developed based on narrow-band LED light source technology. The spectral resolution of the system was 20nm over 420--680nm, with spatial resolution better than 2μm and an imaging range of 520μm × 416μm under 13× magnification. To verify feasibility of the system for clinicopathological analysis, multispectral images of mouse skin squamous cell carcinomas were collected, for both in situ and normal skin tissues. Excitingly, cell structure was clearly observed using the multispectral image system. Spectral information extracted from the image sequence shows that reflectance of the cancerous nucleus has significant difference with that of the normal nucleus in the visible band, allowing the two types of cells to be effectively distinguished. These results indicate that LED illumination-based multispectral imaging systems are promising alternatives to replace traditional, expensive, and complex multispectral imaging systems and play an important role in pathological analysis.