The invention relates to an artificial optimized culture method for sea squirts, microalgae and stichopus japonicus. The artificial optimized culture method for sea squirts, microalgae and stichopus japonicus is a bio-remediation technology for realizing self-purification of a culture water body and a sustainable marine product culturing method by utilizing a biological mutual benefit mechanism of a seawater polyculture system. The bait microalgae are inoculated in culture seawater; and the stichopus japonicus and the sea squirts are put into the culture water body with increased microalgae biomass. The inorganic nutritive salt in the seawater is converted into the microalgae biomass through the bioconversion of the microalgae so as to provide abundant bait for cultured organisms and simultaneously increase the concentration of dissolved oxygen in the water body. The sea squirts filtrate a large amount of sea water to remove grains and excess microalgae in the water body and settle a large quantity of aqueous layer particulate organic matters into a substrate in the form of feces and false faces. The demersal stichopus japonicus with a detritus food habit ingest the organic debris, benthic diatoms and microorganisms in the substrate so as to improve a substrate environment and reduce water body pollution. The artificial optimized culture method for sea squirts, microalgae and stichopus japonicus utilizes the polyculture system to promote the culture proliferation of the stichopus japonicus, carry out the self-purification and remediation of the culture water body, and realize the sustainable development of stichopus japonicus culture industry.