Abstract: Agroecology and food security have a profound impact on the process of agricultural and rural modernization in China, and exploring the co-evolution trends and internal mechanisms of agroecology and food security can help China achieve its goal of becoming a strong agricultural country and exploring possible ways to achieve high-quality synergy between agroecology and food security. This study established an evaluation system for agroecology and food security using 30 provinces (autonomous regions and municipalities, excluding Hong Kong, Macao, Taiwan, and Xizang) in China from 2011 to 2022 as the research target. Initially, the entropy weight method and spatial statistical tools were used to measure the development level of agroecology and food security. The Haken model was used to explore the sequence parameters and cooperation level of the collaborative system, and the Dagum Gini coefficient was used to reveal the spatial differences and sources of the current situation of the cooperation of agroecology and food security. There were three key findings of this study. 1) The level of agroecology and food security in China has generally exhibited a progressive trend. The center of gravity and migration trajectories of agroecology and food security were similar, with both migrating towards the northeast. This suggested that the future may see the northeast direction as a potential source of collaboration between agroecology and food security. 2) Agroecology is the sequence parameter of the synergistic system of agroecology and food security, which dominates the evolution of the synergistic system. This reflects the importance of agroecology in the relationship between food security and agroecology. From 2011 to 2022, the synergy between agroecology and food security in China showed a steady and progressive trend, and it roughly experienced the evolution process of “primary synergy period—intermediate synergy period—advanced synergy period.” The internal difference within the central region was the smallest, indicating that the central region worked together to promote synergy between agroecology and food security. Considering spatial pattern, there are obvious differences in the degree of synergy between agroecology and food security and the mean value showed a distribution pattern of “northeast>central>east>west”. In terms of regions, the internal difference in the degree of synergy in the eastern region is the largest, and Hainan Province has always been at the lowest value in the eastern region, which should be worthy of major attention. 3) Spatial differences in the level of synergy between agroecology and food security are gradually increasing, and regional differences are the main source of the overall differences. The differences between the eastern and western regions were particularly significant. Coordinated development among regions is an important way to resolve the spatial differences between agroecology and food security in China. This study argues that more emphasis should be placed on promoting agroecology systems during the development process of synergizing agroecology and food security systems as they play a more prominent role. Addressing significant regional disparities requires special attention to recognize the importance of agroecology systems in guiding high-quality coordinated development between agroecology and food security systems.