The Southwest Alpine Canyon Area (SACA) in Southwest China-a region characterized by steep terrain, high-altitude valleys, and fragile ecosystems-faces the dual challenge of ensuring grain production and ecological sustainability under global change pressures. This study established an ecosystem vulnerability assessment framework based on the habitat-pattern-function paradigm and employed a four-quadrant analysis to quantify the relationship between grain production and ecosystem vulnerability. The goal is to provide targeted management strategies to ensure regional food security and ecological protection. The results showed that the study area from 2000 to 2022: (1) The total grain yield displayed a spatial distribution pattern of being higher in the southeast and lower in the northwest, with high-yield areas primarily distributed in strip or patch formations along mid- and low-altitude valleys. During this period, grain yield per unit area showed an upward trend, resulting in a total increase of 33.85%. (2) The ecosystem vulnerability index exhibited a fluctuating downward trend, with an overall decline of 6.70%. Areas of moderate vulnerability consistently accounted for the largest proportion. (3) The grain yield increase-ecological improvement zone (Zone IV) covered 50.43% of the study area, with 10.97% under continuous synergistic improvement. The grain yield decrease-ecological degradation zone (Zone II) accounted for 4.25%, including 0.59% undergoing continuous synergistic degradation. The grain yield increase-ecological degradation zone (Zone I) and the grain yield decrease-ecological improvement zone (Zone III), both reflecting trade-off conditions, accounted for 24.64% and 20.68%, respectively, with 10.86% of the area experiencing persistent trade-offs. Notably, 77.58% of the region underwent fluctuating transitions, with the most significant shift (23.67%) occurring from Zone IV to Zone I, indicating a trend from synergistic improvement toward trade-off development. Overall, after years of ecological restoration, the region has shown a general trend of synergy between grain production and ecological conditions. However, localized ecological degradation tied to agricultural expansion persists, necessitating spatially nuanced management interventions.