Because of the low tensile strength, the structure of the masonry pagoda is easy to crack under earthquake,which will cause no uniform shear stiffness along the cross section and the stiffness center deviated from the quality center, and then the coupling vibration is occurred. The coupling relationship of dynamic response for masonry pagodas affected by multi-dimension earthquake is researched, according to the shaking table test for the model of Xuanzang pagoda at Xingjiao temple, the variety rules on the coupling coefficients between acceleration and displacement response changing with the height are compared and analyzed. And the coupling mechanism to seismic response is studied by reference to the damage phenomenon. As results, the plane lateral stiffness changes after the cracking of pagoda affected by multi-dimension earthquake, which leads to the coupling of dynamic responses. The rules are primarily unanimous to coupling coefficients between acceleration and displacement response changing with the height; however, the coupling characters are inconsistent to dynamic response along different direction. The maximum coupling coefficients are about 1.2 under most loading cases. The research conclusions can be referenced to fixing the seismic response analysis for masonry pagoda.