Algal turf scrubber (ATS) is a system for water cleaning, which uses intertidal algae to effectively eliminate nitrogen (N) and phosphorus (P) elements in eutrophic water. Algae is the most important organism in the whole system, and its community structure is closely related to the effect of water purification. Based on the high-throughput sequencing technology of Illumina MiSeq platform, we analyze the diversity of algal samples in ATS system and natural reefs in this study. The results of 18S rDNA show that the ATS system obtains 21390 algal majorizing sequences. Among these majorizing sequences, Antithamnion accounts for 22.79% of the total number, and the rest sequences are classified as Psammodictyon, accounting for 19.07%. Algae in Song Jing, Zhan Nanting and Hou Zhai areas have 88435, 87129 and 106458 majorizing sequences after filtering, respectively. They are mainly Chroodactylon, Mastocarpus and Mazzaella. Both the ATS system and the natural environment samples have the dominant species of Skeletonema and Ceramium. This research shows that the ATS system has similarity and specificity in its community structure compared to the natural reefs, which provides a theoretical evidence for further improving the function of the ATS system.