Agricultural activities exacerbate nitrogen (N) imbalances in the agroecosystem by disturbing the N inputs and outputs, yet the influence of changes in cropping systems on the N balance of agroecosystems remains unclear. In this study, at the field scale, we calculated the N balance of four cropping systems, (1) traditional crops with traditional crop rotation (G-G), (2) vegetables with traditional crop rotation (V-G), (3) vegetables with vegetable rotation (V-V), and (4) greenhouse vegetables (GHV); then analyzed the influence of changes in cropping systems from 1995 to 2015 on the N balances in the agroecosystems in sub-watersheds of the Dagu River. The results indicate that N balances were higher in GHV, V-V, and V-G than G-G, due to significantly higher inputs of N fertilizers and lower N use efficiency (NUE) in vegetable cultivation compared to traditional crops. Driven by economic benefits between 1995 and 2015, V-G, V-V, and GHV replaced G-G in a considerable number of cultivation areas in the sub-watersheds. These changes resulted in an increase of 109.9-170.1% in the N balance in the agroecosystem in the sub-watersheds between 1995 and 2015. In the entire watershed, the total N surplus contribution by V-V, V-G, and GHV increased from 39.3% to 79.1% between 1995 and 2015. These findings suggest that increased vegetable cultivation contributed to the increased risk of N pollution in agricultural production. Thus, there should be a focus on the management of cropping systems to control N loss from agricultural lands.