The balance between agricultural development and maintenance of agro-ecological environment becomes a huge challenge because of global climate changes. Existing literature on the low-carbon pilot policy proposed by the government of China and whether the problems of agricultural development and agricultural environmental protection can be solved or not have not been reviewed. This paper analyzes the impact of low-carbon pilot policies on agricultural eco-efficiency by using SARAR model based on the data of 281 cities in China. Results show the spatial spillover effects between low-carbon pilot policies and agricultural eco-efficiency. The implementation of low-carbon pilot policy can improve agricultural eco-efficiency. Although restrained by agricultural economic development, this policy has disequilibrium effect on agricultural eco-efficiency, has a relatively large impact on agricultural eco-efficiency in western China and other poor areas, and promotes the reduction of agricultural carbon emission. The effect of the implementation of low-carbon pilot policy is affected by the initial agricultural economic development and urban economic conditions. This research aims to improve the agricultural eco-efficiency and enforce the green development of the agricultural economy via the perspective of the low-carbon pilot policy.