A total of 27 specimens were tested under cyclic loading to study the deformation and mechanical behavior of stone masonry joints. The influences of the normal stress level and the mortar strength were investigated. The failure modes, deformation characteristics, hysteretic behavior and shear mechanisms of the specimens were discussed. The test results indicated that all the specimens failed in the shear-sliding mode. The shear behavior of the stone masonry joints could be featured by four stages, i.e., elastic stage, crack propagation stage, shear strength degradation stage and frictional sliding stage. Remarkable vertical compressive deformation was observed in the joint due to the damage of mortar and stone wedges. The vertical deformation of the joints increased with the increase of the normal stress, horizontal displacement and cycles. A hysteretic curve with a rectangular shape was obtained for all the specimens, indicating that the stone masonry joints possess good energy dissipation capacity. Both the shear strength and the energy dissipation capacity were improved with the increase of the normal stress and mortar strength. Finally, a calculation formula for predicting the shear strength of stone masonry joints was proposed. This research could provide reference for the establishment of the micro-mechanical model of stone masonry joints and the seismic performance assessment of stone structures.