The use of wind turbines for energy generation has complex impacts on ecosystems, especially for flying wildlife. Given the importance of birds in many ecosystems and food webs, they are often used as ecological indicators to evaluate the direct (e.g., collision mortality) and indirect (e.g., habitat degradation and loss, low food available) impact of wind farms. To test the effect of wind farms on the nest distribution of magpie (Pica pica), a common bird species in agroforestry systems on Chongming Island, China, the differences in magpie nest density variables and character variables were compared between quadrats inside and outside a wind farm. The relationship between magpie nest character variables and density variables in each quadrat was also examined and the impacts of landscape variables on magpie nest density variables were clarified in each quadrat. From March to December 2019, nest density variables (including total and in-use nest density) were recorded in quadrats inside and outside a wind farm in an agroforestry system on Chongming Island, Shanghai. Three nest character variables and five landscape variables were also recorded in each quadrat. The total nest density and nesting height in the quadrats outside were significantly higher than those inside the wind farm. There was a significant negative correlation between the average nest size in the quadrats and the total nest density, and a significant positive correlation between the average nesting height in the quadrats and both nest density variables. Moreover, farmland shelterbelt network cover and the distance to the nearest wind turbine were significantly positively related to the total nest density, whereas the farmland shelterbelt network cover was significantly positively related to the in-use nest density. These results indicate a negative effect of wind turbines on the nest density of magpies, which could be addressed by the provision of more farmland shelterbelt networks inside the wind farms located in agroforestry systems on Chongming Island, China.