Agricultural non-point source pollution has been a main pollution source in China. So an indicator system for agriculture is needed, which can be used in assessing and supervising the agricultural non-point source pollution. Based on the theory of eco-efficiency and the characteristic of agricultural production, this research designed an evaluation indicator system for Agricultural Eco-efficiency which integrates different factors on economic profit, resource and material consumption and environmental impacts. A rice pot-experiment was carried out. In the experiment, two rice genotypes (Xidao11 and Wuyujin4) of different nitrogen use efficiency were supplied with three N levels (0.05、0.15、0.25 g N kg-1). Ammonia volatilization, fertilizer dose and rice economic yield were analyzed to evaluate and rank the Agricultural Eco-efficiency of the six evaluation indicators by using TOPSIS method which is based on AHP. The result showed that the six evaluation objects varied in economic benefit, resource and material consumption and environmental impacts, and N levels and plant genotypes had a major impact on the Agricultural Eco-efficiency. The evaluation indicator system will help China′s agricultural production mode to change from pursuing unilateral output to a comprehensive, balanced and sustainable one.