The recruitment of dormant Microcystis aeruginosa (DMCs) is an important phase in the formation of Microcystis aeruginosa blooms in aquaculture ponds. When subjected to external environmental stress, such as low temperature, low light, exogenous allelopathic substances, nutrient deficiency, Microcystis aeruginosa cells form DMCs due to damage to the photosynthetic system, phycobilisomes, ribosomes, and other organelles. These DMCs sink to the surface of the sediment to avoid environmental stress. The DMCs are used as seed sources to restart and recruit (repair damaged organelles) once conditions improve. They enter the overlying water, waiting for another outbreak of algal blooms. A higher recruitment rate of DMCs can significantly enhance the interspecific competitiveness of Microcystis aeruginosa, making it prone to population outbreaks and the formation of algal blooms, and vice versa. Therefore, inhibiting the recruitment of DMCs is an effective method for proactively preventing and controlling the outbreak of Microcystis aeruginosa blooms in aquaculture ponds. In order to investigate the effect and mechanism of Pseudomonas lactis BJ-1, an intestinal bacterial strain of Aristichthys nobilis, on the recruitment of resting DMCs in vitro, BJ-1 bacteria were mixed with DMCs and embedded into pond sediment to construct low-concentration bacterial groups (G1), higher-concentration bacterial groups (G2), and high-concentration bacterial groups (G3). The sterile group was used as a control. The recruitment experiment was conducted for 21 days at a water temperature of 25 ℃, light intensity of 15 μmol·m^–2s ^–1, and light-dark cycle ratio of 12 h∶12 h. Mechanism and field verification experiments were performed based on the experimental results. The experimental results showed that the strain BJ-1 continued to proliferate from the beginning of the experiment to the 6th day. After the 6th day, the bacterial concentrations of the low-concentration bacterial group G1, the higher-concentration bacterial group G2, and the high-concentration bacterial group G3 were maintained at (0.99±0.23)×10⁷ cfu·g^–1, (3.40±0.27)×10⁷ cfu·g^–1, and (5.21±0.39)×10⁷ cfu·g^–1, respectively. DMCs began to recruit from the 6th day, and compared with the control group, the content of capsular extracellular polysaccharides (CPSs) in DMCs in G2 and G3 groups decreased significantly, and the photosynthetic efficiency and recruitment rate of DMCs significantly decreased (P＜0.05). In contrast, there was no significant difference between the G1 group and the control group (P＞0.05). At the same time, the experiment found that strain BJ-1 can secrete the metabolite 3-benzylpiperazin-2,5-dione, and its concentration shows a positive linear relationship with BJ-1 bacterial concentration (R² =0.997). The minimum effective concentration of metabolite 3-benzylpiperazin2,5-dione to inhibit the recruitment of DMCs was 0.8 μg·L^–1. The concentrations of 3-benzyl piperazine-2,5-dione in group G2 and group G3 were (0.95±0.24) and (1.41±0.19) μg·L^–1, respectively. At these concentrations, the intracellular reactive oxygen species (ROS) level of DMCs increased significantly (P＜0.05), and the photosynthetic efficiency and recruitment rate of DMCs decreased significantly (P＜0.05). An analysis of differentially expressed genes (DEGs) showed that DMCs encoding photosynthetic genes (psbD1), DNA repair genes (recA), and carbon fixation (ntcA and rbcL) functional genes were significantly down-regulated under higher bacterial concentrations (G2 group), confirming at the molecular level that bacteria BJ-1 can inhibit the photosynthetic efficiency of DMCs. Validation experiments showed that strain BJ-1 can effectively reduce the recruitment rate of DMCs in outdoor pond environments. The experimental results showed that BJ-1 bacteria in the gut of Aristichthys nobilis at higher concentrations (≥3.40×10⁷ cfu·g^–1) can inhibit the photosynthetic efficiency of DMCs in vitro by reducing the CPSs content of DMCs and secreting the metabolite 3-benzylpiperazin-2,5-dione, ultimately hindering the recruitment of DMCs. The experimental results provide new evidence for “controlling algae with Aristichthys nobilis” and also provide new ideas for preventing and controlling Microcystis aeruginosa blooms in aquaculture ponds.