Route planning to evade potential pollution holds critical importance for aquaculture vessels. This study establishes a fish-feed pollutant drift model based on the Lagrangian particle tracking algorithm and designs four sets of sensitivity experiments in the East China Sea. The research investigates the impact of model input uncertainties on the drift trajectory, centroid position, and sweeping area of the fish-feed pollutants. Numerical results indicate that the uncertainty in the background flow field significantly affects the uncertainty in the centroid position and sweeping area in the numerical simulations. Specifically, when a 35% random error is added to the background flow field, the centroid shift distance reaches its maximum, and the sweeping area also attains its largest value. The uncertainty in the background wind field affects the centroid position of particles but to a much lesser extent compared to the background flow field. When considering only the uncertainty of the background wind field, the sweeping area does not significantly differ from the control experiment as the uncertainty of the background wind field increases. The initial release position has little effect on the drift direction of the fish-feed pollutants but does affect the drift distance; it has minimal impact on the trajectory but significantly affects the final position of the pollutant centroid. By analyzing the model uncertainties, this study reveals the key factors influencing the drift of fish-feed pollutants. This information is crucial for aquaculture vessels in planning routes, considering environmental factors, and reducing potential pollution risks.