To investigate the influence of the number of inlet pipes on the characteristics of flow field and the discharge of solid particles such as bait residue and fish feces, STAR-CCM + was used to analyze the flow of field distribution in a ship-based aquaculture cabin under the conditions of two and four inlet pipes, thus optimizing the inlet pipes of the ship-based aquaculture cabin. Furthermore, a three-phase flow model (solid–liquid–gas) was established to determine the movement characteristics of similar solid particles of residual bait and fish manure in the cabin, while the emission performance of solid particles was analyzed. Finally, the formation of solid particles in the center of the aquaculture cabin was simulated. The simulation results show that the effect of flow field is better with two inlet pipes, and the discharge volume of the bottom outlet has little impact on the emission of solid particles. Findings from this study can serve as a reference and basis for the design and optimization of the aquaculture cabin of an aquaculture vessel.