Karst mountain agricultural landscapes are vital socio-ecological systems supporting food security, rural livelihoods, and biodiversity conservation. Despite their importance, their sustainability is jeopardized by intrinsic biophysical constraints, including shallow soils, fractured topography, and erratic hydrology, which are further exacerbated by anthropogenic and climatic stresses.These factors jointly lead to ecological fragility and limited productivity, complicating land-use planning and sustainable management. Yet, most existing ecosystem health assessment frameworks fail to capture the complexity and stress-driven dynamics of karst systems.To address this gap, we propose a multi-dimensional framework (S-VORC) that integrates stress, vitality, organization, resilience, and contribution to assess agricultural ecosystem health under land degradation conditions. Using the Miaoling Mountains in Southwest China as a case study, we assessed spatiotemporal dynamics of agricultural ecosystem health from 2000 to 2020, drawing on diverse environmental and socio-spatial datasets. Results show a modest but consistent rise in the Agricultural Ecosystem Health Index (AEHI) from 0.469 to 0.488, although most areas remain in a sub-healthy state and vulnerable to disturbance. Geomorphic variation strongly influences spatial patterns: flatlands exhibit notable improvement, while peak-cluster depressions and plateau zones remain low in health. Obstacle analysis identified five primary limiting factors: inadequate soil and water conservation, steep slopes, low agricultural investment, and high human disturbance. Based on health status, terrain types, and stressor intensity, we delineated five ecological restoration zones and proposed tailored strategies such as eco-friendly farming, agroforestry restoration, and multifunctional land use.This study provides a transferable framework for land degradation diagnosis and restoration-oriented zoning in fragile karst regions, offering practical insights for sustainable land management and policy intervention.