The submerged fermentation of Cordyceps militaris for cordycepin production and mycelial growth was investigated in this study. Three natural materials of brown rice paste (BRP), beerwort (B), and soybean meal juice (SMJ) were used for fermentation of C. militaris in shaking flasks. The effects of the ratio of three natural materials on dry mycelium weight (DMW) and on cordycepin yield (CY) were analyzed. D-Optional mixture design was used to optimize the ratio of these materials. Compared with the signal culture, the higher mycelial growth and cordycepin production were obtained in mixture. The analysis of Design Expert 6.0 indicated that BRP, B, and SMJ very significantly influenced (P < 0.001) DMW and CY of C. militaris, respectively. The highest DMW (18.96 g/l) and CY (2.17 mg/g) were both obtained at a ratio of 53:6:42. The experiments' results indicated that the above mixture of these natural materials by D-optional mixture design can be used as a proper medium for the growth of mycelium and the production of cordycepin.