With the increasing risk of people and economies being subject to meteorological disasters, it is of great importance to analyse the spatio-temporal variation of these disasters. In this paper, the possible impacts of meteorological disasters on rice yields in Jiangsu Province, southeast China was studied. A total of 17 rice meteorological disaster indices (RMDI) during 1961–2012 was calculated and analyzed. The spatial distribution of RMDI indicated that south Jiangsu should be classified as a high-intensity zone for heat stress, while north Jiangsu should be classified as a high-intensity zone for precipitation extremes and chilling injury. Changing trends of RMDI were detected by the Mann-Kendall test. Precipitation extremes and heat stress indices presented increasing trends, while the chilling injury indices showed decreasing trends. Correlation analysis between rice yield and RMDI with the first difference method and climate-induced yield method showed that precipitation extremes had more dramatic negative effects than the other two types of meteorological disaster. Principal components analysis provided additional information about the regional differences of changes in meteorological disasters. Jiangsu could be divided into three regions (south, middle, and north) with different and changing patterns for RMDI. Also the Western Pacific Subtropical High Intensity Index and the Pacific Decadal Oscillation had significant influences on these changes. These findings could provide a scientific basis for the prevention or reduction of rice meteorological disasters in Jiangsu Province.