[Objective] Exploring the driving factors and improvement paths of agricultural ecological efficiency (AEE) in the main grain producing areas of China is the foundation for guiding different regions to adapt to local conditions and promoting high-quality agricultural development. [Methods] This study constructed a super-efficiency slacks-based measure (SBM) model with non-expected outputs to calculate the AEE of the main grain producing areas from 2005 to 2020, and used trend analysis methods to explore its spatial differences and trends of dynamic changes. It then used Geodetector to explore the driving factors of the spatiotemporal changes of AEE, and ways to improve AEE. [Results] (1) The AEE values in the main grain producing areas showed a fluctuating upward trend, while the areas with medium and high efficiency values shifted from north to south. Overall, the three major river basins showed a trend of Yangtze River Basin > Yellow River Basin > Songhua River Basin; The center of gravity of AEE of the main grain producing areas was mainly concentrated in Shandong Province, with a migration trajectory from north to south. (2) From the perspective of endogenous factors, agricultural machinery input was the inherent dominant factor in the differences in AEE in the main grain producing areas, and the interactive combination of agricultural natural resource input and machinery input was the key driving factor; From the perspective of exogenous factors, economic factors had the strongest driving effect on AEE in the main grain producing areas, and the interaction of external factors enhanced the explanatory power to the spatiotemporal changes of AEE. (3) Based on the driving factors, we identified three paths for improving AEE: endogenous driving, dual driving, and resource integration. [Conclusion] The overall development of AEE in the main grain producing areas of China was improving, but regional differences still exist. In order to achieve sustainable agricultural development, it is necessary to strengthen the popularization and application of agricultural mechanization and intelligence, optimize the allocation of agricultural natural resources, and develop characteristic agriculture according to local conditions.