Linear conjugated internal gear pump plays a key role in hydraulic system, and its efficient pressure transmission characteristics make it widely used in engineering field. In this paper, the effects of axial clearance and radial clearance on leakage and flow field of linear conjugate internal gear pump are analyzed by means of computational fluid dynamics simulation. The results show that the variation of mating clearance has a wide and significant influence on the flow field characteristics of gear pump, in which the axial clearance is the main factor causing leakage, accounting for 80% of the total leakage. Specifically, when the axial clearance increases from 0.03mm to 0.07mm, the output flow rate decreases by 20.81%, the average pressure decreases by 33.15%, and the volume fraction of the gas generated by cavitation increases by 0.021. In contrast, the setting of the same radial clearance only resulted in a 0.69% decrease in output flow, a 2.76% decrease in average pressure, and a 0.005 increase in the volume fraction of the gas produced by cavitation. In addition, the study also found that the main matching clearance leading to the change of flow rate in the pump is the axial clearance. A modest reduction in the axial clearance helps to increase the fluid speed in the pump, thereby enhancing the overall efficiency of the pump. These results provide useful theoretical support for the design and optimization of linear conjugate internal gear pump, which is helpful to improve its performance and reliability in hydraulic system.