The invention discloses a shrimp ecological culture and a polyculture method based on facility microalgae culture, including preparing corresponding microalgae and shrimp fry; then putting them into a culture tank for culture; The cleaning control system monitors the breeding ponds; finally, the breeding is continued; the cleaning control system includes an algae recording unit, a data recording unit, a content detection unit, a single database, a data prediction unit, a single shrimp acquisition unit, a processor, a display unit, It is recommended to generate a unit and a management unit; the present invention uses the cleaning control system to monitor the number of microalgae in the breeding pond in real time, and also combines the growth of shrimp, the number of breeding days and the relevant feeding amount to reasonably predict the corresponding time. The number of microalgae will reach the corresponding upper limit, and according to the number that reaches the upper limit, it will be determined whether local targeted cleaning or overall cleaning is required; it is easy to treat differently.