Improving circulating water utilization efficiency is significant for thermal power plants to reduce costs and increase operational efficiency. This study chose denitrifying bacteria (Denitrobacillus licheniformis EM1) as the microbial agent to investigate its anti-scaling and anti-corrosion performance in the circulating cooling water system from the coal power plant. The calcium carbonate deposition test and coupon test results indicated that denitrifying bacteria could increase the scale inhibition rate of the cooling water system by approximately 25.23% and the corrosion rate from 0.0773 to 0.1074 mm/a. Surface characterization and microbial community analysis were employed to explore the underlying mechanism. Acid production from metabolism and bacterial community shift were speculated to be the main contributors to the anti-scaling capacity of the denitrifying bacteria. This study provides a deeper understanding of the anti-scaling mechanisms of functional strains in microbial agents. This will assist in the advanced development and application of microbial agents in scaling control.