In order to study the propagation law of stress waves in rock mass with filled joint, the propagation law of stress waves in jointed rock mass was analyzed by theoretical and numerical simulation methods. Firstly, the propagation equation of stress wave in joint rock mass was deduced by time domain recursion method, and the filled joint is further simplified as displacement discontinuous model. Subsequently, the stress waves propagation in filled jointed rock mass was simulated by UDEC program, and it is found that the theoretical and numerical results are in good agreement. Finally, the propagation characteristics of stress waves between filled joints were analyzed. The results show that when the stress wave normally incident on the filled joint, compared with the stress wave length, the filled joint thickness is small, and the filled joint can be simplified into a joint model without considering the thickness. The influence of joint space on the energy transmission and reflection coefficient can be divided into three intervals by two critical values, when the joint space is large enough, the energy transmission and reflection coefficients tends to be stable. Between the joint groups, the stress wave will produce multiple transmission and reflection phenomena, and the different positions vibration velocity of the joint rock mass is superimposed by the stress wave.