The invention discloses a prawn ecological culture and polyculture method based on facility microalgae culture. The prawn ecological culture and polyculture method comprises the following steps of preparing corresponding microalgae and prawn seeds; then putting the microalgae and the prawn seeds into a culture pond for culture; carrying out feeding in the later culture process, and carrying out culture monitoring on the culture pond by means of a cleaning control system; and finally, continuously carrying out breeding. The cleaning control system comprises 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, a suggestion generation unit and a management unit. By means of the cleaning control system, the number of the microalgae in the culture pond is monitored in real time, meanwhile, the growth condition of prawns, the number of culture days and the related feeding amount are combined to reasonably predict when the corresponding microalgae can reach the corresponding upper limit value, and according to the number of the microalgae reaching the upper limit, whether local targeted cleaning or integral cleaning is needed or not is judged; and differential treatment is facilitated.