Abstract: A mechatronic axial pump has been widely used for the energy-saving machinery in sustainable agriculture. This study aims to explore the influence of the clearance leakage on the flow field structure in the mechatronic axial pump. The RNG k-ε turbulence model was also utilized to carry out the transient numerical simulation using ANSYS CFX software. The full flow field of the pump was then obtained in the different flow conditions (1 674~2 510 m³/h). Specifically, a systematic analysis was implemented on the pump pressure, turbulent kinetic energy, and vortex volume field distribution. Radial velocity and impeller efficiency were determined to establish the relationship between rotor friction loss and leakage with the flow rate. The leakage flow was finally clarified in the flow fields of mechatronic axial pump. The results show that the special structure of the stator-rotor clearance part was dominated in the efficiency of the whole mechatronic axial flow pump, compared with the traditional. The main reason was that the operating torque of the stator and rotor was greatly contributed to the friction loss power of the rotor and the total shaft power. 19.1% of the pump shaft power was accounted for the mechanical friction loss power on the outer wall of the rotor at rated operating point. There was the increase in the proportion with the increasing flow rate. The leakage and backflow of the clearance and the mixing effect in the main flow area of the blade were extend the low flow pattern to the main flow area of the internal flow channel of the impeller, thus reducing the operating efficiency of the pump. Therefore, the collaborative design of the motor and impeller was required for the energy saving in the mechatronic axial flow pump, in order to minimize the power lost from the rotor friction and then meet the requirements of hydraulic performance. There was the fluid flow through the motor stator-rotor clearance leakage back to the impeller inlet, the formation of jets, the localized area of high turbulent kinetic energy, strong vorticity, and high radial velocity near the edge wall of the impeller inlet. The inflow conditions were seriously disturbed to increase the hydraulic loss for the low efficiency, such as the uniform inflow at the impeller inlet and the assumption of cylinder independence. The closer to the wheel flange position was, the greater the effect was. A mutually constraining and promoting relationship was formed in the leakage and return flow velocity, as well as the pressure difference between the inlet and outlet of the return flow. Importantly, this relationship was also determined as the internal characteristics of the leakage and returns between the stator and rotor clearances of the pump. At the same time, the amount of leakage, the size and degree of influence of the leakage on the flow field structure were negatively correlated with the flow rate. The leakage flow rate of clearance was reduced to minimize the damage to the flow field at the impeller inlet. The finding can provide a strong reference to improve the performance of mechatronic axial flow pumps.