In order to find out the salinization mechanism of shallow and deep groundwater in Nantong area, all sorts of hygro-chemical coefficients and variation diagrams were used to analyze the salinization mechanism of shallow and deep groundwater in the study area. The results show that, in the central and western parts of study area, the hydro-chemical evolution of deep groundwater is controlled by traditional water rock interaction, the increase of TDS in eastern coastal area, especially around the area of Yinyang Town, is the result of salt leaching from paleo marine strata. As for the shallow groundwater, the increase of TDS in the most areas far from the sea is mainly connected with the effects of dissolved salt and evaporation. Influenced at some degree by the modern seawater intrusion, the TDS in coastal area, especially in the Yinyang Town and Haiyan Town in the southeast corner, was significantly increased. According to these change characteristics of groundwater hydro-chemical in the study area, some measures of improving the groundwater system were put forward: develop and utilize high TDS groundwater reasonably to increase the amount of regional water resources and enhance the storage capacity, mitigating potential threats to deep fresh water resources; increase the exploitation amount of salt water gradually to improve saline and alkaline land step by step, having positive significance for soil and water resources utilization and ecological environment improvement in the long term.