Axial piston pumps are the key component in power hydraulic systems. Flow and pressure ripple signals, which can reflect the flow dynamics of the axial piston pump, are important information sources for condition monitoring. Therefore, the characteristics of flow and pressure ripple signals should be investigated for further condition monitoring and fault analysis. However, measuring high-frequency flow ripple directly can be difficult, and the pressure ripple is not only affected by pump dynamics but also affected by the transient pressure wave propagation. However, in practical applications, the hydraulic pipeline system is complex due to the space constraint of the equipment, and the influence of the pipeline system cannot be ignored when modeling pressure ripple. This paper proposes a novel two-stage method for fault simulation of the pumps that considers the influence of the pipeline system on the pressure ripple. Firstly, the surrogate pipeline model with free parameters is calibrated using ITA to capture the characteristics of the complex practical pipeline system. Secondly, the calibrated model is applied to the fault simulation of axial piston pumps. A detailed 3D CFD model of the pump is built up, and the flow ripple at the pump outlet from the numerical model is used as an approximation of the real flow ripple of the pump, which serves as one of the boundary conditions of the surrogate pipeline model. After calibrating the model, the CFD model of the pump is used to simulate internal failures in the pump. Two failure cases are studied: a faulty slipper and a faulty cylinder. The simulated signal of the proposed model matches the experimental signal well under the healthy and faulty conditions, which confirms the effectiveness of the proposed method.