The utilization of algicidal bacteria for the control of harmful algal blooms (HABs) is a promising technology for ecological remediation. In our most recent publication, a novel strain of Brevibacillus sp. was isolated and proved to have significant algicidal activity and stability against Microcystis aeruginosa. In order to verify the algicidal effect of the strain in the practical application scenario, the algicidal efficacy of Brevibacillus sp. under conditions close to water in the environment was investigated. Results indicated that the algicidal threshold of Brevibacillus sp. culture was 3‰ inoculation concentration, and the removal rate of M. aeruginosa reached 100%. The process of Chl-a degradation followed a first-order kinetic model, which could be used to predict the degradation effect of M. aeruginosa in practical applications. Additionally, the inoculation of Brevibacillus sp. culture introduced additional nutrients, some of which remained in the water. Furthermore, the algicidal substances demonstrated good sustainability, with a removal rate of up to 78.53% at 144 h after three repeated uses. At 12 h, the algicidal substances caused a 78.65% increase in malondialdehyde (MDA) content in M. aeruginosa compared to the control group, thereby triggering the antioxidant system of M. aeruginosa. Moreover, algal cell fragments were observed to aggregate. This study provides a promising direction for treating cyanobacterial blooms using algicidal bacteria in practical applications.