Production of cordycepin by Cordyceps militaris batch fermentation was investigated under various fermentation styles. Two-step shake-static fermentation strategy was proposed to achieve the optimal cordycepin production. It can be assumed that cordycepin production is linked to the development of aerial hyphae and conidiophores by analyzing the results of kinetics and morphology of C. militaris fermentation. Massive aerial hyphae and conidiophores accumulation requires two conditions: adequate C. militaris biomass as an essential material foundation and the environmental condition, static fermentation in this case, which can induce cellular differentiation to form aerial hyphae and conidiophores. The specific mycelia growth rate was higher with sufficient nutrition and dissolved oxygen in shake fermentation, and the specific cordycepin production rate was higher in static fermentation. Under two-step shake-static fermentation, a lot of C. militaris cells were obtained in shake stage and the development of conidiophore was activated in static stage, followed by the accumulation of cordycepin. Therefore, cordycepin production reached 2.62 g/L.