Global warming impacts agricultural grain security production in China. We investigated the time series relationship between rice yields and meteorological factors, which are not directly analyzed using traditional multiple linear regression analysis. We obtained rice yield data from the Statistical Yearbook of Jiangsu Province and meteorological data from the China Meteorological Data Sharing Service Network for the period 1978 to 2010. We applied continuous wavelet transform, cross-wavelet and coherent-wavelet methods to analyze changes in rice yields related to meteorological factors such as sunshine hours, precipitation and temperature during rice vegetative and reproductive growth stages. Our results show that the proportion of rice yields affected by meteorological factors in Jiangsu Province decreased from 1978 to 2010 because the ability to withstand weather disasters improved. The continuous wavelet transform period characteristics of rice meteorological yields and meteorological factors such as sunshine hours, precipitation, temperature, the highest temperature, the lowest temperature,and day/night temperature difference are almost similar. Our cross-wavelet and coherent-wavelet transform analyses indicate that the phase difference relationship between rice yield and meteorological factors is complex during seedling tillering, booting development, and blossom fruiting stages. During the seedling tillering stage, an increase in sunshine hours increases rice yields, and an increase in precipitation decreases rice yields. During the blossom fruiting stage, an increasing amount of sunshine hours and large day/night temperature differences increase rice yields; small day/night temperature differences decrease rice yields. To mitigate the effects of global warming, rice cultivation procedures need to change. Land use supervision and management as well as rural land consolidation and high-standard basic farmland construction should be strengthened, farmland water conservation facilities need to be improved, and crop sowing times should be adjusted. Technological devices to predict extreme weather disasters should continue to improve and new biotechnology techniques should be implemented to ensure that rice yields are high and are not severely affected by climate change. Cross wavelet analysis methods can accurately analyze the relationship between meteorological factors and the rice yields; such analysis also helps to predict rice yield outcomes from current meteorological data. Our results enable officials in government agricultural departments to make informed decisions while implementing new agricultural policies related to the storage and harvesting of rice.