Abstract: Against the backdrop of pollutant transport and sedimentation (e.g., uneaten feed and fecal matter) in culture tanks of aquaculture workboats, which is triggered by liquid sloshing from roll and heave motions under wind-wave excitation, this study explored the impact of coupled roll-heave excitation parameters (sloshing period, amplitude) on the self-cleaning hydrodynamic characteristics of culture tanks. The objectives were to enhance pollutant removal efficiency, optimize water quality, and minimize energy consumption. The experimental design aligned with operational scenarios of aquaculture workboats, conducting tests under a 70% liquid loading rate with a four-inlet water supply configuration. By merging Particle Image Velocimetry (PIV) and pollutant collection experiments, the study analyzed pollutant accumulation and flow field distribution characteristics. Results showed a positive correlation between self-cleaning pollutant collection efficiency and coupled excitation amplitude, and an inverse correlation with excitation period. The shortest collection time occurred at a 4 s sloshing period with 2.5° (roll) and 30 mm (heave) amplitudes, while the longest occurred at 8 s with 0.5° (roll) and 10 mm (heave)—an 85.8% difference. Roll amplitude impacted collection performance more significantly than heave amplitude. Shortening the sloshing period and intensifying coupled excitation optimized flow fields, expanding high-velocity regions and central vortices, enhancing turbulence, and improving collection efficiency. This study elucidates the governing laws of coupled roll-heave excitation on self-cleaning hydrodynamics, providing theoretical support for optimizing aquaculture workboat self-cleaning performance. The findings enable precise regulation of water exchange cycles to reduce energy consumption, advancing the green transformation of fisheries in line with carbon peak and neutrality goals. This research enhances deep-sea aquaculture sustainability through efficient pollutant management and drives high-quality marine economic development via energy-saving, eco-friendly practices.