Multi-spectral imaging is commonly used in biomedical field to detect and recognize targets, which are in a low contrast with their background. Highly integrated multichannel light-emitting diode (LED) devices enable tuning the spectral contents of the illumination in an accurate and compact fashion, and hence make multi-spectral lighting more easily achievable even in a microscope. Besides the light source, the light mixing system is also a key to realize it. Existing light mixing devices available for multi-spectral LED lighting systems are both costly to manufacture and intricate in design, making them a challenging solution to create. This work proposes a design of multi-spectral lighting system for microscopic imaging, which can achieve a high uniformity in the effective area of illumination in terms of both the illuminance and chromaticity. Simulation results first demonstrate that the designed lighting system consisting of two rods, both containing a frosted emitting surface, managed to reduce the non-uniformity to less than 0.05 for both the illuminance and chromaticity. Experiments with a real prototype show highly uniformly illuminated microscopic images of tissue section samples. Moreover, the pathogenic fungi in the infected tissue section samples can be highlighted by the superposition of multi-spectral images. These experimental results indicate that the designed multi-spectral LED lighting system can improve the quality of microscopic imaging in terms of the illumination and image contrast.