C. militaris is widely used as a nutraceutical in functional foods or a phytopharmaceutical for treating some serious illnesses; selenium, a newly discovered anticancer element in recent years, can significantly enhance the anticancer activity of functional foods. However, most areas of the earth lack selenium. Selenium-enriching cultivation can significantly enhance contents of organic selenium and cordycepin in C. militaris fruit bodies. This study showed a potential method to produce selenium-enriched C. militaris fruit bodies with higher medicinal value than the commonly used wild C. sinensis, selenium supplementation of food and a primary source of cordycepin which had been reported to have great potential as an anticancer compound. The results also suggested a potential way for liquid fermentation to produce selenium-enriched C. militaris products, especially to enhance cordycepin production.