The quantity and spatial pattern of farmland has changed in China, which has led to a major change in the production potential under the influence of the national project of ecological environmental protection and rapid economic growth during 1990–2010. In this study, the production potential in China was calculated based on meteorological, terrain elevation, soil and land-use data from 1990, 2000 and 2010 using the Global Agro-ecological Zones model. Then, changes in the production potential in response to farmland changes from 1990 to 2010 were subsequently analyzed. The main conclusions were the following. First, the total production potential was 1.055 billion tons in China in 2010. Moreover, the average production potential was 7614 kg/ha and showed tremendous heterogeneity in spatial pattern. Total production in eastern China was high, whereas that in northwestern China was low. The regions with high per unit production potential were mainly distributed over southern China and the middle and lower reaches of the Yangtze River. Second, the obvious spatiotemporal heterogeneity in farmland changes from 1990 to 2010 had a significant influence on the production potential in China. The total production potential decreased in southern China and increased in northern China. Furthermore, the center of growth of the production potential moved gradually from northeastern China to northwestern China. The net decrease in the production potential was 2.97 million tons, which occupied 0.29% of the national total actual production in 2010. Third, obvious differences in the production potential in response to farmland changes from 1990 to 2000 and from 2000 to 2010 were detected. The net increase in the production potential during the first decade was 10.11 million tons and mainly distributed in the Northeast China Plain and the arid and semi-arid regions of northern China. The net decrease in the production potential during the next decade was 13.08 million tons and primarily distributed in the middle and lower reaches of the Yangtze River region and the Huang-Huai-Hai Plain. In general, the reason for the increase in the production potential during the past two decades might be due to the reclamation of grasslands, woodlands and unused land, and the reason for the decrease in the production potential might be urbanization that occupied the farmland and Green for Grain Project, which returned farmland to forests and grasslands.