Challenges for achieving food security with an increasing world population are stimulating many stakeholders to consider the impact of climate change on global-regional crop production. One major concern is how the covariations of climate warming and extremes (e.g., ENSO) affect agricultural systems and production. Here, a dual-cropping system in the Huaihe Plain was used as a testbed to address this issue. We found that climate warming during 1982–2013 ha s produced remarkable influences on the dual-cropping agricultural system. For the spring season crop (i.e., winter wheat), a significant negative effect was found with a production loss of ˜6.9 × 10 6 tons due to an elevated T mean (˜2.21 °C) (r=-0.508, p < 0.01), which was associated with water stress. For the summer/autumn crops (i.e., rice and maize), a significant positive effect was found, but with a less substantial production gain (˜1.4 × 10 6 tons), supposedly due to the relaxed temperature constraints (an increased T max of ˜1.28 °C) for high heat resistant crops (r = 0.495, p < 0.01). The phenophase of the crop growing period was shortened by ˜7 days for the spring crop and by ˜4.4 days for the summer/autumn crops with enhanced thermal conditions. Precipitation anomalies, especially those associated with ENSO turning from El Niño to La Niña, imposed an additional serious impact on the dual-cropping system through decreased precipitation in the spring and increased precipitation in the summer/autumn. Potential impacts for the future could be derived from intensification of water and heat stresses, as well as the climate extremes (e.g., ENSO and AAO).