The existing vacuum fish pump is too large and difficult to move, which is difficult to apply to small fishing vessels. However, the development of a small vacuum fish pump is not a single scaling of the existing vacuum fish pump but requires the support of relevant experiments and simulation theories. In this study, a vacuum fish pump suitable for small fishing vessels was developed. Firstly, a numerical model of the internal flow field during the vacuum fish pump’s working process was established using computational fluid dynamics (CFDs) and verified its effectiveness by physical experiments. It is found that the VOF model can well predict the variation of the volume fraction of the liquid phase in the whole calculation area with time during the suction or drainage process of the vacuum fish pump. Then, the internal flow field characteristics of the fish pump under different working conditions were simulated, and the rationality of the design of the fish pump was evaluated according to the numerical results. Finally, a separate physical experiment was carried out on grass carp, carp, crucian carp, silver carp, and bighead carp, respectively, and the capture efficiency and corresponding fish damage rate for different fish were analyzed. The experimental and numerical results show that the vacuum suction fish pump can achieve efficient and automatic suction and transport of live fish.