Hydraulic axial piston motor is one of the fundamental components in hydraulic systems; it is widely used in engineered machine, especially in high-power drive or reciprocating motion, such as hydraulic excavator. For hydraulic axial piston motor efficient planning, in addition designing and controlling are required for system operating safety and efficiency. Simulation delivers an advantage over analytical approaches and allows better understanding of the motor performance. For multi-piston hydraulic motor, one of the simulation methods, distributed parameter model, could analyze the detailed performance in each piston chamber. Therefore, in this study, we investigate the characteristics of hydraulic axial piston motor by setting up a distributed parameter model based on physical prototype, which includes mechanical–hydraulics coupling process. The effects of the dynamic pressure inside the piston chamber, the fluidic compressibility and other related parameters are considered in the coupling process. At the same time, the distributed parameter model of hydraulic axial piston motor was used in the simulation model of hydraulic excavator. The results indicate that in two-way hydraulic axial piston motor, the valve plane should adopt symmetrical structure, and silencing groove set should be put on both ends of the valve plane slots, which could reduce pressure ripple and overshoot in the piston chamber. Furthermore, the torque characteristics are highly affected by the clearance between the piston and the cylinder bore. Through this research, we may have a better understanding about the mechanism of output torque fluctuation in hydraulic axial piston motor, and the pressure ripple and overshoot in the piston chamber due to through-flow area discontinuity between the silencing groove and the ends of the valve plane slots. The model is verified using a nine-piston hydraulic motor in hydraulic excavator.