Cordyceps militaris is widely cultured to produce fruiting bodies for medicinal and health food use. Illumination is an important factor for the growth, quality and production costs. The effects of different light-emitting diode (LED) light combinations on primordia induction, the growth and bioactive substances of fruiting bodies were investigated. The results showed that the monochromatic red or far-red LED failed to induce primordia. Blue light was a must for primordia induction and a red:blue 2:1 with 10% far-red induced the greatest frequency of primordia. Dry weights of fruiting bodies were lower under red and far-red LED treatments. 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.