The invention discloses a fermenting production method of cordycepin, and the method comprises the following steps of: transplanting activated bacterial strain cordyceps militaris into a fermentation tank filled with a fermentation culture medium, wherein the fermentation temperature is 25-28 DEG C, and the stirring rotation speed is 150-180rpm (revolutions per minute); feeding sodium hydroxide solution and hydrochloric acid to control the pH value of fermentation liquor at 5.5-6.0; and when a carbon source is completely consumed, reducing the stirring rotation speed to be 60-80 rpm, and replenishing a water solution containing glucose and adenosine into the fermentation tank by means of intermittent feeding, wherein the whole fermentation time is 200-280 hours. According to the fermenting production method, the pH value of the fermentation process is controlled, and the energy sources and the cordycepin precursor are timely replenished, so that the fermentation process can be kept under an optimum environment, and the fermenting production method is good for the growth of thallus, and good for the transplantation of metabolic flux, therefore, the cordycepin yield can be finally up to 10.0g / L, the production efficiency reaches 0.25g / L / d, and the method is simple in process, lower in environment pollution, convenient to operate, and high in cordycepin yield.