Global water resources are under tremendous pressure influenced by population growth and economic development. Considering that the agricultural sector accounts for the largest consumption and that China is one of the major agricultural countries, this study conducted an impact-oriented water footprint analysis to quantify the environmental burdens of crop production in China from a life cycle perspective. The temporal variation of potential environmental impacts during 2008–2017 was evaluated, and 334 cities in China were used to investigate the spatial characteristics of environmental burdens. Results showed that the environmental burdens were mainly ascribed to direct consumption, fertilizer production, and diesel production. The overall burdens uninterruptedly increased from 2008 to 2015 and then declined in 2016. The decomposition results of temporal variation demonstrated that agricultural economic scale and crop productivity were the largest positive and negative contributors to burden growth, respectively. The burdens exhibited an evident spatial autocorrelation, and high–high agglomerations were mostly located in the North China Plain and Yangtze River Delta due to the superior natural resource endowments and dense population in these regions. Such factors as natural resource endowments (i.e., cultivated land and precipitation), agricultural input intensity (i.e., fertilizer and diesel), and effective irrigation area proportion significantly influenced the spatial variation of environmental impacts at the city level. Therefore, adopting water-saving technologies, strengthening fertilization management, promoting large-scale and mechanized agriculture, and choosing clean alternative fuels are highly recommended to achieve sustainable agricultural development. Furthermore, in consideration of the dominance of high–high clusters in crop production in China, advanced and eco-friendly production technologies should be vigorously incentivized in these regions to enhance their agglomeration and radiation force.