AimsSoil seed banks are critical reservoirs for plant community regeneration, yet their composition, which associates with biodiversity patterns across microhabitats in fragile transition zones, remains poorly understood.MethodsWe investigated the forest-grassland ecotone on the Loess Plateau, China, to disentangle the associations between soil seed banks and plant diversity maintenance by comparing diversity patterns of aboveground vegetation, seedlings, and soil seed banks across abiotic conditions in microhabitats (vegetated patches vs. bare patches).ResultsOur results revealed that soil seed bank characteristics varied significantly with microhabitat types, which in turn corresponded to distinct alpha- and beta-diversity patterns in seedlings and aboveground vegetation. Vegetation patches exhibited higher alpha-diversity than bare patches, with soil properties acting as associated factors. beta-diversity was primarily associated with topographic slope, while showing an inverse correlation with soil seed bank compositional similarity. Different patch types showed distinct correlational patterns: vegetation patches were associated with soil-mediated processes, whereas bare patches were increasingly influenced by climate and topography.ConclusionsOur findings reveal key patterns linking soil seed banks to seedlings and vegetation assembly within heterogeneous habitats, advancing theoretical understanding of biodiversity and seed bank-vegetation relationships and providing a scientific basis for fragile transition zones restoration assessment and management.