Abstract: Based on provincial panel data, and applying the quantile regression model, this paper analyzed the effects of fertilizer application on grain yield in China. Varieties studied in this research include early indica-rice, middle indica-rice, late indica-rice, japonica-rice, wheat and corn. Results show that China’s agricultural fertilizer application has been growing continuously and has exceeded the international safety standard. The intensities of fertilizer on wheat and corn were higher than that of rice. There exists intensity difference between advantage producing areas and disadvantage producing areas and it also exists between eastern China and western China. Descriptive statistical analysis indicates that the strength of fertilizer and grain yield have the same trend. Chemical fertilizers still have positive effects on grain yields while showing significant declining marginal return. In the future, the Government should encourage zero growth of fertilizer application, pay more attention to improve fertilizer efficacy, and keep the balance between grain security and sustainable agricultural development.