<p>Potassium peroxymonosulfate (PMS) is widely used as a disinfectant in shrimp aquaculture, but inappropriate dosing can lead to ineffective pathogen control or toxicity to cultured organisms. This study developed a quantitative framework to optimize disinfection in industrialized Pacific white shrimp (<i>Penaeus vannamei</i>) culture. The approach integrates pathogen inactivation, disinfectant decay, and shrimp safety. Laboratory experiments quantified the inactivation kinetics of PMS against pathogenic <i>Vibrio</i> species. Additionally, we assessed the decay of effective disinfectant concentration under varying water-quality conditions and the acute toxicity to juvenile shrimp. The results showed that PMS exerted a marked concentration-dependent inactivation effect on <i>Vibrio</i> spp., with maximum reductions of approximately 1.70–1.96 log₁₀ for sensitive strains at 2 mg/L. However, at lower concentrations (0.50–1.00 mg/L), <i>V. alginolyticus</i>, <i>V. campbellii</i>, and <i>V. parahaemolyticus</i> showed regrowth after 6–12 h. The decay of PMS-derived residual oxidant followed first-order reaction kinetics and was significantly affected by environmental factors, including temperature, total suspended solids, and chemical oxygen demand. The 96-h median lethal concentration (LC₅₀) for juvenile shrimp was 6.365&#xa0;mg/L. This value corresponds to a calculated safe concentration (SC) of 0.6365&#xa0;mg/L. These datasets were integrated into a system dynamics model that couples <i>Vibrio</i> growth, disinfectant decay, and bactericidal efficacy, enabling dynamic simulation of pathogen suppression and post-disinfection rebound. Model predictions agreed well with independent experimental observations. This study provides a practical decision-support tool to balance <i>Vibrio</i> control with shrimp safety. These results support precision disinfection management strategies for sustainable aquaculture.</p>