Abstract: Systematically revealing the spatiotemporal differentiation patterns of agricultural sustainable development in coastal hilly areas is of crucial practical significance for maintaining the functional integrity of regional ecosystems, safeguarding food security, and stabilizing social and economic systems. This study employed the three-dimensional ecological footprint model to quantitatively analyze the dynamic evolutionary characteristics of the agricultural ecological supply-demand relationship across the coastal hilly areas of Fujian Province from 2012 to 2021, and further conducted a dynamic evaluation of the agricultural sustainable development status of nine prefecture-level cities in this province. The key findings are as follows: 1) The agricultural ecosystems in the coastal hilly areas of Fujian Province were generally under substantial pressure, with the ecological supply-demand imbalance exhibiting an intensifying trend and significant regional differentiation. Specifically, the annual average growth rate of per capita ecological footprint in the nine prefecture-level cities was significantly higher than that of per capita ecological carrying capacity. 2) The coordination between agricultural development and ecological conservation in Fujian Province was inadequate, as economic growth remained highly dependent on ecological resources. The ecological footprints of the four major land types (i.e., cultivated land, forest land, grassland, and water bodies) increased synchronously. Systematic resource overdraft exposed the risk that the traditional intensive development model was approaching its ecological limits, and such imbalance presented distinct regional differentiation: in inland hilly areas, grassland resource consumption was mismatched with the development of animal husbandry; in coastal hilly areas, water area exploitation was inconsistent with the growth of fishery economy, which highlighted the urgency of transforming and upgrading the agricultural production mode. It is evident that the core contradiction of agricultural sustainable development in the coastal hilly areas of Fujian Province stemmed from the superposition of rigid constraints on ecological carrying capacity imposed by terrain limitations, the continuous expansion of resource demand driven by economic development, regional imbalance, and population outflow from mountain areas, which urgently called for development plans tailored to regions. By quantifying the balance status between agricultural resource demand and regional carrying capacity, this study constructed an analytical framework of “problem diagnosis-risk warning-coordination path”, and integrated the ecological deficit warning mechanism with economic coordination paths. This research not only provides a theoretical basis for the agricultural sustainable development in Fujian Province, but also offers practical references for the coordinated development of agricultural ecology and economy in coastal hilly areas under the framework of SDG 15 “Life on Land” and the “Dual Carbon” goals.