Agricultural eco-efficiency is a meaningful index that assess the agricultural sustainable development. Based on the super SBM-DEA approach incorporating agricultural carbon emissions and panel data regression, this study evaluates agricultural eco-efficiency and then investigates the influencing factors in agricultural production zone of Jilin Province. The empirical results show the following: (1) During the observation period, the average agricultural eco-efficiency exhibits a flat “M-shaped” fluctuating trend, a trend of fluctuant growth with phase characteristics, and the agricultural eco-efficiency of each county still has much room for improvement. (2) Significant spatial differences exist in agricultural eco-efficiency across counties. All of the studied counties, except for Nong’an, Huadian, Lishu, Yitong, Gongzhuling, and Qianguo, need to change the input and output structure to optimize agricultural eco-efficiency. (3) The panel data regression model verifies that the agricultural technology extension level, agricultural economic development level, agricultural industry structure, agricultural mechanization intensity and urbanization level have close correlations with agricultural eco-efficiency. (4) The research findings have important implications for policy makers formulating agricultural environmental policies in accordance with the local conditions of various counties.