The noise analysis of a large-scale aquaculture vessel reveals that during its navigation, the primary equipment noise, particularly from the propeller, exerts a notable influence on the aquaculture environment for large yellow croaker. The free surface greatly impacts the noise performance of propellers, which is a significant factor affecting the fish’s habitat. This study adopts the numerical simulation method to analyze the hydrodynamic and acoustic characteristics of the E1619 propeller operating near the free surface. The open-water performance and noise calculations of the propeller are verified through experiments, and the effects of different immersion depths and advance coefficients on the propeller are explored. The results demonstrate that the free surface significantly affects the thrust, torque, and noise of the propeller, especially at shallow immersion depths and low advance coefficients. Surface wave pattern causes the instability and breakup of tip vortices, causing increased thrust and torque fluctuations, reduced efficiency, and significant overall sound pressure levels in the entire flow field. As immersion depth and advance coefficients increase, the interaction between tip vortices and the free surface weakens, wake vortex instability decreases, and noise levels gradually reduce. These analyses and conclusions can guide the design of next-generation propellers for aquaculture vessels to optimize performance near the free surface.