The current environmental and economic challenges of the application of nitrogen (N) fertilizer on crops are not only to provide an adequate food supply but also to reduce the resulting environmental pollution. A comprehensive understanding of the multiple effects of N fertilizer application on crops will help to more accurately guide the application of N fertilizer to meet current challenges, and to promote sustainable crop production. It is widely known that excessive N fertilizer applied to crops can lead to N-related direct environmental effects, including reactive N (Nr) losses, greenhouse gas emissions, and high environmental costs. However, few studies have revealed the hidden indirect environmental effect of crop N fertilizer application and its impact on the net ecosystem economic benefit (NEEB), which may be triggered by a N-crop-pest cascade pathway. In this study, we conducted three-year wheat field experiments at five N fertilizer application rates (0, 70, 140, 210, and 280 kg ha−1) in a city on the North China Plain. Excluding wheat yield and direct N-related environmental effects, the indirect effects of N fertilizer application, including the occurrence of cereal aphids (the most important wheat insect pests), the use of chemical pesticides for pest control, the impacts on the environmental and human health damage costs and NEEB were studied. Our results showed that the abundances of cereal aphids positively correlated with the N fertilizer application rates. At each N fertilizer application rate (70, 140, 210, 280 kg ha−1), 0.447 kg of active ingredients of chemical pesticides (0.222 kg insecticides and 0.225 g fungicides) per hectare per season were used to control insect pests and pathogens, while no pesticides were used at 0 kg ha−1(i.e., no N fertilizer was applied). The environmental and human health damage costs of pesticides for pest control increased $8 per hectare for wheat at four N fertilizer application rates and then reduced NEEB by the same amount. Our work extends previous studies and reveals the indirect negative environmental effect of N fertilizer application on crops triggered by a N-crop-pest cascade pathway. This effect undercuts the contribution of crop N fertilizer application on NEEB.