On the basis of the structural dynamic analysis theory and fluid structure interaction theory ， this paper puts forward the “ improved pseudo three-dimensional ” beam aqueduct computing mode replacing the existing “ pseudo three-dimensional ” beam aqueduct model. In this paper, the model can not only achieve two-way synchronization FSI(fluid structure interaction) of the aqueduct with large sloshing water, but also greatly improves calculating efficiency. So the model can be used for calculating and analyzing the joint multi-span aqueduct considering FSI. In addition, the “ improved pseudo three-dimensional ” can be used to calculate the aqueduct structure with a stiffening rib. One segment of Dongshen Water Supply Aqueduct is analyzed by employing “ improved pseudo three-dimensional model ”， which yields much close results compared those using 3D finite element model. Therefore ， the improved pseudo three-dimensional dynamic analysis method is proved to be a practical static and dynamic analysis method for dynamic analysis and seismic design of large aqueduct structures with high efficiency.