Owing to the lack of dynamic property information and experience in practical application, seismic design of aqueduct has no standard to follow in our country. Study on the seismic mitigation and isolation of large aqueduct is of great practical significance. In accordance with some aqueduct in South to North Water Transfer Project, this paper simulates nonlinear hysteretic restoring force curve of isolation bearing of the lead core rubber aqueduct by bilinear model, compares and analyzes the earthquake response considering the interaction of the aqueduct bridge and the water-body in the aqueduct. The results show that the isolation bearing can reduce the structure ' s response to the earthquake and improve the ability of anti-seismic structure.