Abstract: Systematically revealing the spatiotemporal differentiation patterns of agricultural sustainable development in coastal hilly regions is of crucial practical significance for maintaining the functional integrity of regional ecosystems, safeguarding food security, and stabilizing social and economic systems. Taking the coastal hilly areas of Fujian Province as the study area, this research employed the three-dimensional ecological footprint model to quantitatively analyze the dynamic evolutionary characteristics of the agricultural ecological supply-demand relationship across the province from 2012 to 2021, and further conducted a dynamic evaluation of the agricultural sustainable development status of its nine prefecture-level cities. The key findings are as follows: 1) The agricultural ecosystems in the coastal hilly areas of Fujian Province are 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 is significantly higher than that of per capita ecological carrying capacity. 2) The coordination between agricultural development and ecological conservation in Fujian Province is inadequate, as economic growth remains highly dependent on ecological resources. The ecological footprints of the four major land types (i.e., cultivated land, forest land, grassland, and water area) have increased synchronously. Systematic resource overdraft has exposed the risk that the traditional intensive development model is approaching its ecological limits, and such coordinated imbalance presents distinct regional differentiation: in inland hilly areas, grassland resource consumption is mismatched with the development of animal husbandry; in coastal hilly areas, water area exploitation is inconsistent with the growth of fishery economy, which highlights 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 stems 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 mountain hollowing, which urgently calls for targeted zonal development plans. By quantifying the balance between agricultural resource demand and regional carrying capacity, this study constructs an analytical framework of “problem diagnosis-risk early warning-coordination path”, and integrates the ecological deficit early warning mechanism with economic coordination pathways. This research not only provides a theoretical basis for the sustainable development of agriculture in Fujian Province, but also offers practical references for the coordinated development of agricultural ecology and economy in coastal hilly regions under the framework of SDG 15 “Life on Land” and the “Dual Carbon” strategy.