Abstract: Urbanization is an important factor to impact agricultural ecological efficiency. However, most of the existing studies have discussed the impact of urbanization on agricultural ecological efficiency from a single perspective. Further, these studies are often affected by the impact of exogenous environment or other random factors during the measurement of agricultural ecological efficiency. To analyze the impact of urbanization on agricultural ecological efficiency more comprehensively and accurately, the present study used the three-stage SBM-DEA model, which provides simultaneously evaluation of both the undesirable and desirable outputs, entropy value method, and Tobit model, based on panel data obtained from 13 major grain-producing regions in China from 2009 to 2018. Various models and methods were used to study the impact of urbanization on agricultural ecological efficiency from multiple perspectives based on theoretical analysis. Our results showed that: 1) the impact of exogenous environment and random interference significantly impacted the agricultural ecological efficiency. After excluding these impacts, the agricultural ecological efficiency of the 13 major grain-producing regions in China changed significantly. Additionally, unlike the existing studies, the impact of urbanization on agricultural ecological efficiency too changed, after the effects of exogenous environment and random interference were removed. 2) The agricultural ecological efficiency of China's 13 major grain-producing regions showed a continuous growth trend from 2009 to 2018. The average annual efficiency, after excluding the impact of exogenous environment and random interference, increased from 0.53 in 2009 to 0.80 in 2018. However, there was a big gap in the agricultural ecological efficiency among different regions. For example, in 2018, the agricultural ecological efficiency of Hebei and other regions reached the frontier (1.00), but that of Inner Mongolia was only 0.45. 3) Urbanization as a whole improved the agricultural ecological efficiency. The comprehensive index of urbanization significantly affected agricultural ecological efficiency (at a level of 1%, impact coefficient: 0.60). 4) Various indicators of urbanization differently impacted the agricultural ecological efficiency. The population urbanization rate showed an insignificant negative impact on the agricultural ecological efficiency. The per capita disposable income of urban residents and urban economic density significantly positively affected the agricultural ecological efficiency. The output value of the secondary and tertiary industries, proportion of built-up area and per capita built-up area had significantly negative effect on the agricultural ecological efficiency. To further elucidate the role of urbanization in promoting agricultural eco-efficiency, this article proposed suggestions to modify the relevant policies, based on the research results from three aspects of population, economy, and land urbanization.