In order to obtain a solid-state fermentation grain medium that can simultaneously increase the content of cordycepin, adenosine, and ergosterol in Cordyceps militaris fermented substrate and clarify the enrichment pattern of the three active substances, the composition of culture medium was selected from 7 grains and the ratio was optimized by mixture design using the content of cordycepin, adenosine, and ergosterol as evaluation indicators. Subsequently, the Logistic and Boltzmann models were applied to describe the fermentation kinetics of mycelial growth, substrate consumption, and the production of cordycepin, adenosine, and ergosterol. The results showed that under the optimal formulation was 12.9 g of buckwheat, 5.6 g of oat, and 1.5 g of wheat. Under this condition, the contents of cordycepin, adenosine, and ergosterol reached 1448.87 ± 11.92 mg/kg, 554.50 ± 2.36 mg/kg, and 1019.33 ± 2.88 mg/kg, respectively. The dynamic analysis shows that all five indicators exhibit obvious periodic changes, the coefficients of determination (R2) for all kinetic models were greater than 0.98, and the accumulation curves of the three active substances all show an S-shape. Model predictions indicated that the contents of the three bioactive compounds exceeded 99% of their theoretical maximum values at 27 d of fermentation. The fermented substrate obtained from this study provides new raw materials for the development of C. militaris health food.