Abstract: In recent decades, there has been a high frequency of droughts and floods in China, which affects the agricultural sector as it is more sensitive to climate changes than other industrial sectors. Therefore, this study aimed to evaluate the sensitivity, exposure, adaptability, and vulnerability of China’s agricultural ecosystem to droughts and floods from 1991 to 2019 via selected indicators and index weights determined by the analytic hierarchy process and entropy method. Results show that the drought-sensitive areas of the agricultural ecosystem in China are distributed in the central and southern provinces, such as Hubei and Hunan. The flood-sensitive areas are distributed in the coastal provinces of Hainan, Shanghai, and Jiangsu. Areas with high exposure to droughts and floods are found in the provinces of Gansu, Henan, and Heilongjiang. Areas with low adaptability to droughts and floods are found in the Southwestern provinces of Tibet, Chongqing, Guizhou, and Yunnan. Generally, the drought and flood vulnerability of the agricultural ecosystem in China tend to be weak from the central areas to the other areas, and Henan and Hubei belong to the central provinces with high vulnerability to droughts and floods. Therefore, to recede and adapt to the high vulnerability in the central provinces, the agricultural ecology structure in China should be adjusted according to local conditions, and measures like flexible planting and feeding and crop protection should be adopted to cope with droughts and floods.