China is a disaster prone country, and a comprehensive understanding of change of disasters is very important for China’s agricultural development. In this study, statistical techniques and geographic information system tools are employed to quantify the main agriculture disasters changes and effects on grain production in China during the period of 1990-2011. The results show that China’s grain production was severely affected by disasters including drought, flood, hail, frost and typhoon. The annual area covered by these disasters reached up to 48.7×106 ha during the study period, which accounted for 44.8% of the total sown area, and about 55.1% of the per unit area grain yield change was caused by disasters. In addition, all of the disasters showed high variability, different changing trends, and spatial distribution. Drought, flood, and hail showed significantly decreasing trends, while frost and typhoon showed increasing trends. Drought and flood showed gradual changes and were distributed across the country, and disasters became more diversified from north to south. Drought was the dominated disaster type in northern China, while flood was the most important disaster type in the southern part. Hail was mainly observed in central and northern China, and frost was mainly distributed in southern China. Typhoon was greatly limited to the southeast coast. Furthermore, the resilience of grain production of each province was quite different, especially in several major grain producing areas, such as Shandong, Liaoning, Jilin and Jiangsu, where grain production was seriously affected by disasters. One reason for the difference of resilience of grain production was that grain production was marginalized in developed provinces when the economy underwent rapid development. For China’s agricultural development and grain security, we suggest that governments should place more emphasis on grain production, and invest more money in disaster prevention and mitigation, especially in the major grain producing provinces.