Cordycepin contents in fruiting bodies were significantly higher in red and white (red:blue:far-red 6:3:1) LED treatments, with the increases up to 62% over the fluorescent control. Carotenoids content was significant lower in the red or far-red LED treatment than in other treatments. The results demonstrated the functions of different wavelength lights on the growth and biosynthesis of bioactive substances and that using the low heat release and energy consumption LED lights to replace the traditional fluorescent lights can improve the product quality and increase the contents of bioactive substances. A red to blue ratio of 2:1 with 10% far-red is the optimal light quality for culturing fruiting bodies of C. militaris.