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Abstract Many agricultural regions in China are likely to become appreciably wetter or drier as the global climate warming increases. However, the impact of these climate change patterns on the intensity of soil greenhouse gas (GHG) emissions (GHGI, GHG emissions per unit of crop yield) has not yet been rigorously assessed. By integrating an improved agricultural ecosystem model and a meta‐analysis of multiple field studies, we found that climate change is expected to cause a 20.0% crop yield loss, while stimulating soil GHG emissions by 12.2% between 2061 and 2090 in China's agricultural regions. A wetter‐warmer (WW) climate would adversely impact crop yield on an equal basis and lead to a 1.8‐fold‐ increase in GHG emissions relative to those in a drier‐warmer (DW) climate. Without water limitation/excess, extreme heat (an increase of more than 1.5°C in average temperature) during the growing season would amplify 15.7% more yield while simultaneously elevating GHG emissions by 42.5% compared to an increase of below 1.5°C. However, when coupled with extreme drought, it would aggravate crop yield loss by 61.8% without reducing the corresponding GHG emissions. Furthermore, the emission intensity in an extreme WW climate would increase by 22.6% compared to an extreme DW climate. Under this intense WW climate, the use of nitrogen fertilizer would lead to a 37.9% increase in soil GHG emissions without necessarily gaining a corresponding yield advantage compared to a DW climate. These findings suggest that the threat of a wetter‐warmer world to efforts to reduce GHG emissions intensity may be as great as or even greater than that of a drier‐warmer world.