Eco-efficiency is a tool for sustainability analysis that indicates how to carry out economic activities effectively. This paper assesses agricultural eco-efficiency using data envelopment analysis (DEA) and the Theil index approach. Using basic data of 31 provinces in China during 2003–2013, we analyzed the agricultural eco-efficiency development level and spatial pattern in China. The results show that the agricultural eco-efficiency of only four provinces has been relatively efficient in the entire study period, namely, Zhejiang, Hainan, Chongqing, and Tibet. The results also show that agricultural eco-efficiency was higher mainly in south of the Qinling Mountains-Huaihe River Line and north of the Yangtze River area, that agricultural eco-efficiency is mainly affected by pure technical efficiency, and that highly efficient areas are mainly concentrated in the densely populated areas, i.e., the economic developed areas (except Tibet). The Theil index results show that the agricultural eco-efficiency difference weakened between provinces in China, as did western and northeast regions, but eastern and central regions show a slight upward trend.