The municipal reclaimed water, which often reused in circulating cooling water system, can effectively alleviate the urban water crisis. However, the reclaimed water contains a large number of microorganisms while the water environment in circulating cooling water system allows the micro-organisms to further increase. Therefore, circulating cooling water system faces slime, corrosion and other microbial problems. In this work, the microbial population structure of circulating cooling water makeup by municipal reclaimed water was investigated by using modern molecular biology DNA technology. Our results demonstrated that at the level of family, there were 17 kinds of suspended microorganisms in municipal reclaimed water, in which the dominant strain belonged to Proteobacteria, Betaproteobacteria, Methylophilales, Methylophilaceae. For the circulating cooling water without chemical agents, 13 kinds of suspended bacterias and 36 kinds of immobilized bacteria were detected, in which the dominant strain respectively was Comamonadaceae and Pseudomonadaceae which belonging to Proteobacteria Betaproteobacteria. After adding chemical agents, the number of suspended bacteria increased to 26 kinds and the distribution of bacteria species was even more. And the dominant strain become Staphylococcaceae, which belonged to Firmicutes, Bacilli, Bacillales, the reason for this was the sharply increase of TOC and TP after adding scale and corrosion inhibitors. Corrosion of instrumentation and pipe network systems caused by microorganisms is particularly complicated in circulating cooling water systems and even in whole reclaimed water utilization systems. The corrosion mechanism and corrosion process caused by different microorganisms are different. Therefore, it is very important to explore the composition of microorganisms in reclaimed water to study the corrosion of microorganisms. Based on the study of microbial population structure in municipal reclaimed water, this paper explores the microbial population structure and dominant species in the water in response to the specific situation in which reclaimed water is reused in the circulating cooling water system. At the same time, it also provides some research suggestions for the future research on the corrosion caused by microorganisms in the reuse of recycled water.