A method and system for removing harmful pollutants in cultivation water by using an attaching algal flat system comprise the steps of acquiring biomass of attaching algae in natural water, and time that it takes to cultivate attaching algae to develop specific biomass; acquiring growth rate of the attaching algae, and recording light intensity, retention time and water depth in the case of maximum growth rate; building a relationship of harmful pollutant removal rate to the retention time, pollution load and the biomass of the attaching alga; determining treatment capacity of cultivation water, and building the attaching algal flat system; introducing the cultivation water to the attaching algal flat system, and running the attaching algal flat system to remove harmful pollutants in the cultivation water, such as ammonia nitrogen, heavy metals, environmental hormones, and antibiotics; harvesting attaching algae, and clearing the attaching algal flat system. By optimizing a growth environment required to breed attaching algae in water during circulation and maintaining maximum growth rate of algae, the harmful pollutants in the cultivation water are removed, aquatic cultivation environment is improved, aquatic product is improved, and quality safety of aquatics are guaranteed from the origin.