Based on analysis of morphological structure and hydrological characteristics of Poyang Lake, four generalized patterns of the morphological structure and hydrological characteristics were presented for hydrodynamic numerical simulation to solve these problems of moving boundary resulted from two changes of the number and positions of estuaries due to high amplitudes of water level changes of Poyang Lake, which are lacustrine facies pattern in high water level, water-rising pattern in medium water level, water-falling pattern in medium water level,and fluvial facies pattern in low water level. The internal moving boundary problem of each morphological structure and hydrological characteristics pattern was settled by using the existing dry-wet grid method on computational fluid dynamics. Thereby, an integrated method to deal with complicated moving boundary due to high amplitudes of water level changes was presented for shallow lakes. In order to develop Poyang Lake hydrodynamic modeling system, an algorithm based on the open-source component of MapWinGIS for the boundary fitted orthogonal curvilinear grid of each morphological structure and hydrological characteristics pattern was developed for the needs of hydrodynamic simulation and results visualization. Two main modules of Poyang Lake hydrodynamic modeling system, the module of data pro-post processing and data interaction and the module of hydrodynamic numerical simulation were integrated in the form of loose coupling using the programming platforms of Visual C# and Visual Fortran. In order to verify the simulation effect and precision, an experimental simulation for Poyang Lake with gauged data in December 6-14, 1999 was carried out using developed Poyang Lake hydrodynamic modeling system. The simulated results show that not only the simulation time is obviously shorted but also the simulated effects, which include lake water boundary, water level, depth and current, are better because of the use of integrated moving boundary method.