Parallel axial piston pump has simple structure and high efficiency. Unilateral waist groove of valve plate in axial piston pump has double valvewindow. Piston conducts oil inlet and outlet conversion through valve-window. The dead volume and flow area in piston chamber change to produce large pressure shock and noise, affecting service life of parallel axial piston pump and system stability. After analyzing kinematics relations of piston pump, valve plate area and deputy leakage of activity, single piston model was established by multidisciplinary software AMESIM. Based on this, the work establishes the whole pump simulation model. For single piston model, the geometry relation of transition region was optimized to obtain reasonable valve structure: the deflection angle in 7° and damping groove depth angle in 6°. After that, test platform was built to conduct experimental verification of whole pump pressure fluctuation. The accuracy of the model was proved, and with the increase of load pressure, the output pressure fluctuation became larger.