This paper analyzes the characteristics of the NPS nitrogen pollution of the groundwater in Guoyuan Village, Pudong District, Shanghai. And the associated effects on the surface and groundwater around the study area are discussed in detail based on the successive observed data, DNDC and L-THIA model. The results show that both of the surface and groundwater are polluted so seriously that they are not suitable to drink. The average content of total nitrogen in surface water is 6.3 mg/L and 16.85 mg/L in the groundwater, and both of them attribute to Grade V surface water standard (≤2.0 mg/L) according to the national standard(GB 3838-2002). It is concluded that the nitrogen pollution comes mainly from the fertilizer of the peach orchard based on the further modeling analysis. Therefore, reasonable adjustment of fertilization measures and project may be an effective and practical approach to control the nitrogen pollution around the peach orchard.