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Human land use intensification is increasing biodiversity loss worldwide through fragmenting contiguous natural habitats into spatially isolated patches of varying sizes. However, it is poorly known as to how the area and isolation of patches operate to jointly alter biological community composition for contrasting land use types, particularly for belowground organisms. Oceanic islands that vary in human activities provide an ideal model system for examining how patch area and isolation affects community dissimilarity resulting from land use change. We conducted a paired sampling design that included both natural woodland (i.e. land covered with woody plants, including trees and shrubs) and degraded grassland for each of 20 islands differing in area and remoteness in the largest archipelago of Eastern China. We used this design to investigate how island area and remoteness shape the community dissimilarity of soil fauna between woodland and grassland directly and indirectly through changing climatic and habitat properties. The dissimilarity of soil fauna communities for each island was estimated by measuring total beta (β) diversity and its turnover and nestedness components between woodland and grassland. We found that land use change did not decrease taxa richness but did alter community composition overall. There was no relationship of island area with community dissimilarity when it was estimated by total β-diversity, due to contrasting responses of its turnover and nestedness components to island area. Soil faunal compositional dissimilarity between woodland and grassland along the area gradient was mainly related to the gain and loss of unique taxa in grassland. On small islands, nestedness was the primary contributor to total β-diversity, due to a loss of soil fauna taxa as habitats shifted from woodland to grassland, and suggests that natural habitats serve as refuges for soil organisms. Meanwhile on larger islands, turnover was the main contributor to total β-diversity, suggesting that diverse land uses can increase biodiversity across habitats. Additionally, high habitat differences combined with favorable climatic conditions (such as low wind speed) on larger islands facilitated species turnover but diminished nestedness. Meanwhile island remoteness did not affect total β-diversity or its components, but it did significantly enhance the negative impact of land-use conversion on the abundance of larger-bodied taxa. These findings suggest that island area, and therefore landscape patch area, play a crucial role in shaping the dissimilarity of soil faunal communities that stem from human land use change. Our results highlight that partitioning total β-diversity into its turnover and nestedness components is essential for understanding the impact of land use change on soil faunal community composition in fragmented habitats.