Selenium-enriched Cordyceps militaris fruit bodies are industrially cultivated as functional food or medicinal food in China and southeast Asia. However, composition of selenium compounds and distribution of the main bioactive components are still unknown. In the selenium-enriched fruit bodies, the main soluble selenium compounds of low molecular weight were identified as SeMet (selenomethionine), and the main selenium compounds bound in proteins were identified as SeMet and SeCys (methylselenocysteine). Trace minerals as Se (selenium), Zn (zinc), Fe (iron) and the main active components as adenosine, cordycepin and carotenoids were mostly distributed in the terminal of fruit bodies, while P (phosphorus) and K (potassium) were evenly distributed in the fruit bodies. The results indicated that terminal of the fruit bodies should be the better materials for production of advanced functional food. So cultivation of relatively short and thick fruit bodies with bigger terminals deserves further research.