In ecologically vulnerable agro-pastoral ecotones, understanding the interplay between landscape patterns and fractional vegetation cover (FVC) is crucial for sustainable management. This study focuses on the agro-pastoral ecotone of Inner Mongolia, utilizing 1990-2020 remote sensing data and integrated methodologies including the dimidiate pixel model, landscape pattern index analysis, and coupling coordination degree model. It systematically examines the spatiotemporal evolution characteristics and interactive relationships between fractional vegetation cover and landscape pattern indices. The results indicate that: (1) During 1990-2020, fractional vegetation cover displayed fluctuating upward trends with a distinct spatial distribution pattern of "higher in the northeast and lower in the southwest", exhibiting "northern degradation versus southern improvement" regional differentiation; (2) High-coverage areas exemplify the "green fragmentation paradox", while low-coverage regions experienced "contiguity loss" crises, reflecting the transformation process from contiguous bare land to fragmented sandy land in the desertification frontier zone; (3) Landscape pattern indices demonstrated high fitting degrees with fractional vegetation cover, showing continuously rising fragmentation and declining aggregation in coupling coordination, yet encountering severe imbalance in 2000. Based on these findings, we propose two key recommendations. One is a spatial zoning strategy with differentiated priorities: controlling degradation in the northwest and optimizing ecological quality in the southeast. The other is implementing landscape pattern optimization to enhance connectivity and counteract fragmentation, which is vital for regional ecological security and sustainable development.