Cordyceps militaris is a type of food and medicinal species and is widely cultured in Asia. Substrate and strain are important factors for the production of fruiting bodies and bioactive components contents in fruiting bodies of C. militaris. This study aimed to select the excellent strains and suitable substrates by six strains of C. militaris cultivated on rice, wheat, and tussah (Antheraea pernyi) pupae. The results showed that the rice and wheat were suitable for fruiting body formation of strain CM3, with yields of 23.19 and 19.07 g per bottle, and biological efficiency of strain CM3 were 62.26% and 54.48%, respectively, which were significantly higher than other strains. Tussah pupae is suitable for fruiting body formation of strain CM9, with fruiting body length, yield, and biological efficiency of 5.57 cm, 6.80 g per each, and 291.70%, respectively, which were significantly higher than other strains. The content of adenosine in fruiting bodies of strain CM9 cultivated on tussah pupae was 2.62 mg g-1, followed by that of strain CM3 on rice of 2.51 mg g-1. The content of cordycepin in fruiting bodies of strain CM4 cultivated on wheat was 5.68 mg g-1, followed by that of strain CM9 on wheat of 5.41 mg g-1. To improve the product quality and the contents of bioactive components, C. militaris strains and substrates should both be considered, that is, different strains should be appropriate for different substrates.