The North China Plain (NCP) is the most important agricultural production area in China. Crop production in the NCP is sensitive to changes in both climate and management practices. While previous studies showed a negative impact of climatic change on crop yield since 1980s, the confounding effects of climatic and agronomic factors have not been separately investigated. This paper used 25 years of crop data from three locations (Nanyang, Zhengzhou and Luancheng) across the NCP, together with daily weather data and crop modeling, to analyse the contribution of changes in climatic and agronomic factors to changes in grain yields of wheat and maize. The results showed that the changes in climate were not uniform across the NCP and during different crop growth stages. Warming mainly occurred during the vegetative (preflowering) growth stage of wheat and maize, while there was a cooling trend or no significant change in temperatures during the postflowering stage of wheat (spring) or maize (autumn). If varietal effects were excluded, warming during vegetative stages would lead to a reduction in the length of the growing period for both crops, generally leading to a negative impact on crop production. However, autonomous adoption of new crop varieties in the NCP was able to compensate the negative impact of climatic change. For both wheat and maize, the varietal changes helped stabilize the length of preflowering period against the shortening effect of warming and, together with the slightly reduced temperature in the postflowering period, extend the length of the grain-filling period. The combined effect led to increased wheat yield at Zhengzhou and Luancheng; increased maize yield at Nanyang and Luancheng; stabilized wheat yield at Nanyang, and a slight reduction in maize yield at Zhengzhou, compared with the yield change caused entirely by climatic change.