The karst and fractured ground are common geological conditions during construction of foundation pit of Metro; and the complex hydrogeological environment is the main cause of disasters. The lithology, characteristics of karst fracture and relative water content of foundation pit of Shangyuanmen Metro Station in Nanjing are studied by analysis of hydrogeological data, geophysical exploration and connectivity test method. The foundation pit can be divided into 4 areas according to the types of surrounding rocks and fractures; and then relevant countermeasures are proposed. Good effects have been achieved by selecting proper grouting materials and construction technology. The practice shows that the comprehensive analysis method of water gushing of foundation pit near river in fractured ground used in case study is feasible and rational, so as to reduce the cost and achieve good effects.