When studying the coupling coordination relationship between agricultural eco-efficiency and urbanization, it is crucial to consider food security, especially in a populous country like China. This paper focuses on 31 provinces in China as the research units, covering the time period from 2000 to 2020. Based on the concept of agricultural eco-efficiency, an evaluation index system was developed to include undesirable outputs (carbon emissions), and agricultural eco-efficiency scores were calculated using the SBM–DEA model. An urbanization evaluation index system, covering six dimensions and twelve indexes, was constructed. A comprehensive index of urbanization is measured using the entropy method. On this basis, a coupling coordination model was applied to quantify the relationship between agricultural eco-efficiency and urbanization at the provincial scale in China. The results showed that the agricultural eco-efficiency of all provincial units in China exhibited an overall trend of improvement. Average efficiency followed a spatial pattern of majority grain-consuming areas > grain production–consumption balance areas > majority grain-producing areas. The level of coupling between agricultural eco-efficiency and urbanization is generally low. Currently, no regions have reached the stage of synergy or high-level coupling. Most regions are currently in an antagonistic stage with a coupling degree of 0.3 < C ≤ 0.5. The classification of coupling coordination levels changed from four levels of "severe imbalance", "moderate imbalance", "mild imbalance", and "primary coordination" to "moderate imbalance", "mild imbalance", "primary coordination", and "intermediate coordination". The level of "severe imbalance" disappeared, the level of "intermediate coordination" appeared, and the level of "mild imbalance" became the largest scale level. From the perspective of food security, the proportion of grain production in the categories of "primary coordination" and "intermediate coordination" was less than 10%, and these provinces never achieved self-sufficiency in food production. The proportion of grain production at the "mild imbalance" level reached 62.4%, while the per capita grain production at the "moderate imbalance" level reached 846.7 kg. Provinces with lower levels of coupling coordination have stronger food security capabilities. It can be observed that the weaker the coupling coordination between agricultural eco-efficiency and urbanization, the higher the food self-sufficiency. Based on the research results above, we discussed strategies to enhance agricultural eco-efficiency in majority grain-producing regions by focusing on technological progress and technical efficiency. Additionally, we analyzed approaches to achieve grain self-sufficiency in regions characterized by a high level of coordination between agricultural eco-efficiency and urbanization, considering both production and trade dimensions. [ABSTRACT FROM AUTHOR]