Taking inter-storey and peak displacements of an aqueduct frame structure as a control index, the reliability model of the aqueduct structure controlled by horizontal displacement subjected to a small earthquake was built. On the basis of the relative specifications, the limit values of inter-storey and peak displacements were put forward. According to the statistical characteristics of design parameters, the reliability controlled by displacement of the aqueduct structure system under a small earthquake has been studied using the method combining Monte Carlo simulation with finite element. A new reliability analysis and design method of aqueduct structure under earthquake action was put forward.