Stressed by complex internal flows, fish has a special locomotion feature different from the cruise in a jet fish pump. Based on the high-speed photography and dynamic mesh technologies, the present paper proposed a new numerical simulation methodology to study the impact of fish locomotion on the internal flow in a jet fish pump. The results show that both single fish and fish shoal can cause wall static pressure peaks. Fish causes a rise of static pressure around its body and the pressure increment increases as primary flow rate grows. Fish shoal can result in a decrease of the measured value of mixed flow rate, yet the locomotion of single fish shows no significant effect on it. As the rise of axial velocity difference between internal flow and fish, a low axial velocity region closed to fish body downstream expands. Fish locomotion has a significant effect on the recirculation region. The recirculation region firstly breaks and then forms again when fish passes through this region. The investigation results are helpful to understand the change of flow field in jet fish pumps disturbed by fish and provide reference for design and optimization of jet fish pumps. This new methodology also provides a solution for simulating of moving object in flow fields. •A new numerical simulation methodology is proposed to study fish locomotion in a jet fish pump.•Effects of fish locomotion on the pressure distribution are discussed in a jet fish pump.•Impacts of fish shoal transportation on measured values of flow rates are analyzed.