A biological method was developed for reusing urban reclaimed water in circulating cooling water systems (CCWS), in which the compound microorganism preparation (CMP) mainly included nitrobacteria, Bacillus subtilis, photosynthetic bacteria and Thiobacillus denitrificans, was used to control the scaling, corrosion and biofouling of CCWS. The abundant carbon, nitrogen and phosphorus in urban reclaimed water met the needs of microbial growth. Compared with chemical agents, CMP had the advantages of high efficiency, no additional chemicals and being more economical. The research results showed that CMP improved water quality and decreased ammonia nitrogen (NH3-N) and chemical oxygen demand (COD). The concentration ratio of CCWS reached 3.87 using CMP. The corrosion inhibition rate of CMP and the removal rate on biofouling achieved 99.69% and 22.21%, respectively. The mechanisms of CMP to control scaling, corrosion and biofouling were discussed, and the surface characteristics and chemical compositions of corrosion products and biofouling were analyzed.