Abstract:[Objective] The strains with high-yield for active compounds such as cordycepin and cordycepic acid were screened from Cordyceps militaris (C. militaris) collected in Shaanxi Hualongshan National Nature Reserve. [Method] Three strains LH3, LY1, and LY9 of C. militaris were isolated and identified. The yields of the primary active compounds, hydroxyl radical scavenging activity, and cellular oxidative protection activity in the extracts of the mycelial and fermentation broth of each strain were determined. [Result] The yields of cordycepic acid, crude polyphenols, and crude polysaccharides, which were the main active compounds of C. militaris, were the highest in the mycelia extract of strain LY9, with values of 2.94, 28.79, 65.01 mg/g, respectively, while the yield of cordycepin was the highest (0.53 mg/g) in the fermentation broth extract of strain LY1. Both the extracts of mycelia and fermentation broth of strain LY9 exhibited significant hydroxyl radical scavenging (IC50 values of 0.923 mg/mL and 0.619 mg/mL, respectively) and cellular oxidative protection activities, with cell viabilities of 82.65% and 78.46% at a mass concentration of 1.00 mg/mL. When being cultivated for fruiting bodies, only strain LY9 successfully formed fruiting bodies, with higher yields of cordycepic acid, crude polyphenols, and crude polysaccharides than those in its mycelia. [Conclusion] Strain LY9 exhibits high yields of active compounds, outstanding antioxidant and cellular oxidative protection activities, and a stable ability to form fruiting bodies with high mass fractions of active compounds. Therefore, it has the potential to be domesticated for commercialization of C. militaris.