Sustainable crop production is a significant challenge in China. To achieve this goal, it is necessary to evaluate environmental impacts related to the sustainable development of crop production by integrating scientific and practical indicators. Therefore, this study employed emergy and index decomposition analysis approaches to assess the environmental impacts of non-point source pollution and the overall performance of crop production in China’s 31 provinces. First, the emergy flow of emission impacts and two new indicators, the emergy sustainability index and the emergy-based pollutant-producing coefficient, were proposed to comprehensively measure crop production performance from 2012 to 2015. The results demonstrated that the environmental impacts of non-point source pollution (EIN) were predominantly attributed to total nitrogen and phosphorus contents and mulching film residuals, which substantially increased the total emergy used and reduced the sustainability of crop production in each province. The ratio of EIN plus purchased resources (F) to total emergy used (U) were consistently greater than 80% in all 31 provinces, while the ratio of local resources including the emergy of local renewable (R) and non-renewable resources (N) to the total emergy was relatively small, accounting for less than 20% in all provinces. Then, a logarithmic mean Divisia index decomposition method was applied to identify the key driving forces influencing the evolution of EIN. The decomposition analysis indicated that the economy factor had a major promoting effect on EIN growth in all provinces except Beijing and Shanghai. Intensity and technology factors had a limiting effect on EIN growth. These findings provide valuable insights for developing appropriate crop production policies that consider local conditions.