Seismic study of canyon sites has always been one of the important fields of seismic studies because of massive structures such as dams that are built in such sites. Jointed rock mass in rock canyon sites is one of the main site effects that can change the seismic waves. In this research, we studied the influence of this factor on the scattering of seismic waves. To fulfil this goal, we employed a coupled method combining the finite element method in the near field with boundary elements in the far field. To simulate the behaviour of jointed rock mass, we used the linear elastic model. Based on the results of the numerical analyses, jointed rock mass could have significant effects on the seismic waves in some special conditions. These conditions are the angle of incident wave, the thickness of layers and the material properties of the jointed rock mass. So it is necessary to consider this factor in the seismic structure design in the canyon sites.