The invention relates to a method for constructing a specific pathogen-free penaeid shrimp culture system, which comprises the steps of adopting comprehensive treatment of culture water for avoiding the entry of pathogens; introducing selected oocystis borgei into a penaeid shrimp culture pond for constructing a good microalgae community structure, and using a microalgae-controlled water environment to reduce the concentration of injurious factors, such as ammonia nitrogen, nitrite nitrogen and the like in a water body, improving the water quality, eliminating stress factors, improving the content of dissolved oxygen in the water and leading the environment of the water body to be in the good dynamic balance state for a long time. A system of the oocystis borgei, rhodopseudanonas palustris and phycomycete is utilized for inhibiting the growth of vibrios during the early stage, the middle stage and the late stage of culture; and schmackeria dubin is utilized to intake microalgae, thereby controlling the number of the microalgae in the water body and eliminating the adverse impacts of rapid proliferation of the microalgae on a culture environment. Penaeid shrimps have the advantages of specific pathogen-free property, rapid growth, strong disease resistance, strong stress resistance, short culture period, large and uniform formed size, high output, good investment efficiency and the like.