The invention provides a production method of a microbial fish guano. The production method comprises the following steps: fermenting materials, drying, crushing, and adding inorganic fertilizer and solid photosynthetic bacteria. Because all the organic fertilizers are fermented, the invention has a good water solubility and can fast culture pelagic organisms in the water substance, thereby providing adequate feedstuff to fishes and shrimps; the invention improves the culture water environment, and reduces the harmful substances in water, such as ammonia, nitrogen, nitrite, hydrogen sulfide and the like; the invention can realize the intensive alternate-breeding culture and greatly increase the yield per unit culture area, and the yield can be increased by more than 40% based on the current service condition; and the invention has the advantages of low cost, safety, high efficiency, environmental friendliness and no pollution, thereby ensuring the production of pollution-free green food.