Based on the background of the south-to-north water diversion project, the high damping rubber isolation technology was used for the isolation design of the aqueduct, the codes and design experiences of building and bridge were refered. A finite element dynamic model of the aqueduct is established, in which the fluid-structure coupling was considered by Housner model, witch was used to analyze the dynamic characteristic and seismic response of isolated aqueduct. The results show that the first three vibration modes of the isolated structure are the isolation vibration. The structural vibration modes of the high damping rubber isolated and the lead-core rubber isolated aqueduct are the same, and their natural frequencies are basically the same. The seismic characteristics of the ground motion exert a great influence on seismic response. The closer the characteristic frequency of seismic wave gets to the fundamental frequency of the structure, the greater the response of the aqueduct body and support will be, and the more obvious effects the isolation bearings will have. Under three-direction ground motion input, the peak responses of isolated aqueduct can be refered in design .