To address biodiversity degradation in Nationally Important Agricultural Heritage Systems, this study integrates multi-temporal remote sensing data (2000–2023) with the Biodiversity Maintenance Function (BMF) and InVEST Habitat Quality (HQ) models. We assess ecological changes in the Beijing–Tianjin–Hebei (BTH) region and 14 nationally recognized heritage systems. A dual-factor HQ–BMF coupling matrix was developed to trace ecological trajectories shaped by both natural and anthropogenic influences. Results show that (1) regional BMF followed a non-linear trend of increase, decline, and rebound between 2003 and 2023. The mean value rose from 0.1036 in 2003 to 0.1397 in 2023, despite intermediate fluctuations. In contrast, HQ declined steadily from 0.8734 in 2003 to 0.7729 in 2023, reflecting a continuous loss of high-quality habitats. (2) Nearly all heritage systems experienced phased BMF fluctuations—an initial rise, subsequent decline, and eventual recovery. At the same time, HQ showed a continuous decline in 8 of the 14 systems, indicating that more than half of the systems experienced sustained habitat degradation. (3) The HQ–BMF matrix revealed strong spatial heterogeneity. By 2023, only one site remained in a “dual-high” zone, while another had fallen into a “dual-low” condition, suggesting localized ecological degradation. These findings provide quantitative support for conservation strategies, ecological compensation, and land-use regulation in agricultural heritage systems.