Fertilizers are an essential input in agriculture as they can enhance crop yields. However, their use also poses significant environmental risks. To thoroughly explore the intensity of fertilizer use and its potential threats to the ecological environment, this study analyzed the environmental risks of fertilizer use from a temporal and spatial perspective based on fertilizer application data in China from 1978 to 2022. Additionally, the contribution of fertilizer application in Chinese farmland to greenhouse gas N2O emissions was quantified using IPCC emission factor methodology. The results indicated that fertilizer application intensity and N2O emissions in China initially increased and then decreased from 1978 to 2022. Despite the implementation of various fertilizer control measures at the policy level, such as the Zero Growth of Fertilizer Action in 2015 and the Efficiency-Increasing Action for Reducing Fertilizer Use in 2022, the intensity of fertilizer application in China still exceeded international safety standards by 1.33-fold in 2022, reaching 298.79 kg/hm2. Furthermore, N2O emissions amounted to 50.17 × 104t, accounting for 16% of China's total agricultural greenhouse gas emissions that year. Correlation and regression analyses demonstrated that with increasing fertilizer application, crop production exhibits an inverted U-shaped growth trend, indicating limited effectiveness of high-intensity fertilizer use in increasing crop yields. These findings highlight the profound greenhouse effect resulting from the use of agricultural nitrogen fertilizer. Therefore, this study proposed technical and policy-level mitigation measures to address the issues caused by excessive fertilizer application, aiming to provide insights for controlling agricultural non-point source pollution and preserving the agroecological environment.