The use of phosphorus-containing chemical corrosion and scale inhibitors has been found to result in excessive phosphorus discharge and an inability to reduce the high concentration of CODcr in the circulating cooling water, thereby making it challenging to comply with increasingly stringent sewage discharge standards. This study aims to assess the practicality of utilizing biological corrosion and scale inhibitors in coal power plants’ operation, as well as investigating the correlation between water quality indicators and microbial communities during the conversion period. The data illustrates that, in comparison to the chemical method, there is a decrease in turbidity of the circulating water from 19.44 NTU to 9.60 NTU, a reduction in CODcr from 71.55 mg/L to 45.47 mg/L, and a drop in TP from 2.35 mg/L to 0.38 mg/L. Microbial community analysis during the transition period reveals that microorganisms rapidly establish a new equilibrium in the circulating water, sediment, and fiber ball, resulting in significantly different microbial community structures. The relative abundance of corrosive microorganisms such as Flavobacterium, Pedomicrobium, and Hydrogenophaga is significantly diminished in the circulating water, whilst the abundance of anaerobic microorganisms like Anaerolineaceae and Rhodopseudomonas in the sediment also declines. Conversely, there is an increased presence of microorganisms associated with contaminant degradation, such as CL500-3 and SM1A02. These findings suggest a decrease in the risk of system corrosion and an enhancement in contaminant degradation capability. This study provides evidence supporting the replacement of chemical agents with biological agents in circulating cooling water systems, contributing to more environmentally friendly and sustainable practices.