A dynamic characteristic equation is given, in which two basic unknown variables(aqueduct displacement ui and water pressure p) are let in, and the coupling format(ui,p) with finite element analysis (FEA) of fluid-solid interaction(FSI) derived from energy variational principle is adopted. And on the basis of FEA’s format(ui,p) of the FSI system, a dynamics model describing a aqueduct body-water-pier of aqueduct-fundation-ground coupling system based on the format (ui,p) of FSI system is established, the dynamic properties of the aqueduct are obtained by using asymmetric algorithm, and the dynamic response of the aqueduct under the action of dynamic loads is calculated by adopting the implicit-explicit integration algrithm. The calculated results indicate that by adopting the fluid-solid coupling system with FEA based on the format (ui,p), the calculation model is simplified and its calculating accuracy improved, and mean while, the laws of dynamic characteristics and respone of the aqueduct structure under different discharges are obtained.