In China, dramatic changes of land use since 1980 have induced environmental and socioeconomic problems threatening food security. Therefore, improving sustainability of land use in China is of utmost importance, especially in agricultural regions. So far, few investigations have analyzed sustainability at small scales in China. Here, we propose a methodological framework for assessing the sustainability level of main agricultural regions in China on regional and county levels. We distinguish four sustainability categories: environmental, economic, social, and comprehensive sustainability. Two methods of measuring sustainability were used: (1) the balanced performance method that measures balanced performance among different aspects and (2) the aggregate achievement method that measures aggregate achievement of all aspects. Spatial variation maps of sustainability across counties were produced using a geographic information system, and the limiting factors in each region were identified. Results show that the two methods give highly different values of sustainability levels. The balanced performance method yields lower sustainability values ranging from 0.06 to 0.57, whereas the aggregate achievement method yields higher sustainability values ranging from 0.11 to 0.87. Such differences have not been addressed in previous studies. Using the balanced performance method, the Sichuan Basin is the most comprehensive sustainability region with a 0.05 level, while Xinjiang is the least comprehensive sustainability region with a 0.01 level. Using the aggregate achievement method, the middle reaches of the Yangtze River and Jianghuai region is the most comprehensive sustainability area with a 0.46 level, whereas South China is the least comprehensive sustainability area with a 0.31 level. Sensitivity analysis showed that Songnen and Sanjiang Plains were more sensitive to the indicator selection and aggregation rules. Scale effects were not observed for sustainability assessment at the regional level.