The modernization of agriculture and rural areas and the integrated development of urban and rural areas reinforce each other. Taking Henan Province, where agricultural development is prominent and urban-rural relations have undergone drastic changes, as an example, this study constructs a multidimensional index system based on the coupling mechanisms of agricultural modernization and urban-rural integration. Using the entropy weight method, the coupling coordination degree model, and the obstacle degree model, this study analyzes the spatiotemporal coupling characteristics and obstacle factors of agricultural modernization and urban-rural integration at the county level in Henan Province in 2002, 2012, and 2021. Additionally, targeted development recommendations are proposed for different coupling coordination stages. The results indicate that: 1) The levels of agricultural modernization and urban-rural integration at the county level in Henan Province have increased significantly, with growth rates of 114.12% and 144.06%, respectively. Regional disparities have gradually narrowed, and counties of the same type exhibit significant spatial agglomeration characteristics. 2) The coupling coordination degree of agricultural modernization and urban-rural integration has improved markedly, transitioning from an “imbalanced” state in 2002 (0.505) to a “coordinated” state in 2021 (0.734). Counties of the same coupling coordination type display a strong tendency toward “convergent” agglomeration. 3) The primary obstacles to coupling coordination have shifted from a balanced stage to an agricultural modernization-dominated stage, with agricultural industrial benefits emerging as a key obstacle. Meanwhile, significant variations in obstacle degrees exist among different coupling types. (4) In terms of development strategies, counties in the barely coordinated stage should focus on enhancing agricultural modernization and promoting diversified development; counties in the moderately coordinated stage should prioritize food security and advance the equalization of basic public services between urban and rural areas; counties in the well-coordinated stage should foster new drivers of development and establish a modern urban-rural governance system.