There has been a wide range of applications on establishing hydrogeological structure model in nearly horizontal strata. However, application of GMS on hydrogeological structure model in intruded rock-occuring region is rare. The purpose of this study is to establish the hydrogeological structure model with GMS software in Wushan Copper mine in Jiangxi province and explore the application of this model in rock-occuring region. The results indicate that: (1) It's feasible to construct hydrogeologic structure model in intruded rock-occuring strata areas, in which intruded rock’s Horizon ID is set as 7 and inserted between Q and T1d2-T2j strata in Wushan mine ; (2) The model clearly reflects spatial structure relationship among aquifers; (3) Visualization model can depict split and combination of aquifer flexibly, rotation of any section and any direction, cutting section and other functions, and related geological and hydrogeological information.