Aims <p>Habitat loss significantly threatens global biodiversity and ecosystem functionality. Forest biomass, encompassing both aboveground and belowground, is key indicator of ecosystem functioning. However, the effects of habitat loss on belowground biomass and the factors driving its distribution in fragmented habitats remain unclear.</p> Methods <p>We conducted a field planting experiment involving four woody plant species with distinct functional traits (e.g., shade-tolerance and dominance) across edge and interior regions of 11 islands within a subtropical anthropogenic archipelago in China. Belowground biomass accumulation was measured in the growth areas of each species, including root biomass of the planted species and other plants. We then tested the effects of island area, edge effects, and abiotic variables (e.g., soil physicochemical properties and topographic attributes) on belowground biomass.</p> Results <p>Our results demonstrate that mean belowground biomass increases significantly as island area decreases below a certain threshold. Altitude, litter layer depth, soil bulk density, and soil depth significantly affect belowground biomass. Specifically, belowground biomass accumulation in the growth areas of shade-intolerant species increases significantly as island area decreases before certain threshold. Additionally, mean belowground biomass in edge habitats was significantly greater than in interior habitats, particularly in the growth areas around dominant and shade-intolerant species.</p> Conclusion <p>These findings suggest that habitat size along with soil physical properties, edge effects, and the species shade tolerance play a critical role in shaping belowground biomass accumulation in fragmented landscapes. This study underscores the importance of integrating belowground biomass dynamics into assessments of ecosystem functionality in fragmented habitats.</p>