The theory of island biogeography predicts the number of species on islands is balanced by species colonization and extinction through the function of island area and isolation. It indirectly assumes the habitats on islands are homogeneous. However, for some species, especially insects, the microhabitats may be more vital for their survival on islands. Here we assessed the jointed effects of microhabitats (canopy density, depth of leaf-litter, cover of leaf-litter, cover of moss, cover of vegetation and number of seedling) and island attributes (island area and isolation) on ants’ species richness and abundance on 33 island fragments in the Thousand Island Lake, China. We placed pitfall traps to capture ants and collected the microhabitats around each pitfall trap. We divided all ants based on diet (predator and omnivore) and used Principal components analysis (PCA) on microhabitats data and extracted the PCA axis as new microhabitats variables. We then used Generalized Linear Mixed Model to test the relationship between species richness (and abundance) and PCA axis and island attributes. The first PCA axis (PC1) represent microhabitats with high light availability, low amount of leaf-litter and high level of understory vegetation, whereas the second PCA axis (PC2) represents site with moderate light availability and lower amount of understory vegetation. We found overall and omnivore species’ abundance increase with PC2, indicating that ants with abundant group tend to utilize the microhabitats with more barren or bare ground with a great amount of moss as some omnivore species could directly feed on moss. However, both richness and abundance of predator species increase with island area and decrease with PC1. These results indicated that predator species are more vulnerable of habitat fragmentation, as smaller fragments support less predator species which in line with tropic theory of island biogeography. Meanwhile, predator also prefer the bare ground but with typical requirements of more canopy cover and less moss cover. Our results indicated that the important of microhabitat of fragmented habitats in determining the ant’s species richness and abundance. Additionally, predator species are at higher tropical level and their richness and abundance are essential to the ecosystem health. Thus, conservation effort should focus on those habitats that can support more predator species in fragments.