Subsidence wear is inevitable in a reciprocating compressor system, but how to induce body vibration is not clear. We investigated the dynamic behavior of a reciprocating compressor system with subsidence fault considering a flexible piston rod. The flexible piston rod was modeled as a cantilever beam. The dynamic model, in which the influence of the subsidence size, variational cylinder pressure, impact effects and piston rod flexibility are taken into account, was established. Influences of the four parameters including subsidence size, vertical force of flexible piston rod, cylinder pressure and crankshaft speed were analyzed in the dynamic response. Numerical results reveal that with the change of the four parameters, the existence of subsidence fault has a significant effect on the displacement, velocity and acceleration of the crosshead in the transverse direction, but only conspicuously affects the acceleration in the longitudinal direction. In addition to cylinder pressure, the larger the values of the other three parameters, the greater the influences. The cylinder pressure is a time-varying working load. Not only the cylinder pressure but also the open/close time of the valves and change rate of the pressure all affect the dynamic behavior of the system with subsidence. Meanwhile, the change in the vertical force of the flexible piston rod has a remarkable effect on the jump position of the crosshead, but the effect of other parameters is not obvious. In addition, the changes of parameters produce obvious influences on the impact force and the impact range of the crosshead. The stability of the reciprocating compressor system was studied using Poincaré portraits method. The result shows that the system with subsidence fault has chaotic behavior.