Temporal β diversity reflects the changes in community composition through time, which usually results from species losses and gains. However, the temporal dynamics of β diversity caused by extinction and colonisation remain unclear. Here, we partitioned the temporal β diversity of bird communities into extinction and colonisation components by using two periods of bird dataset in the Thousand Island Lake, China. We further assessed the effects of island area and isolation on dynamics of avian β diversity. We found that the bird species colonisation increased, but bird extinction decreased the overall avian β diversity on the islands spanning ten years. These results indicate that local extinction results in more homogeneous bird communities while the colonization of new species simultaneously leads to heterogeneous, offsetting each other. We also found that neither differences in area nor inner distance between pairwise islands significantly affected the total temporal changes in β diversity of birds. However, the partitioning indicated that the extirpation-resultant homogenisation and heterogenization were both lower between islands with larger differences in sizes. The further partitioning on temporal changes in avian β diversity via six types of extinction and colonisation processes showed that both loss and gain of different rare species on similar-sized islands decreased β diversity (biotic homogenisation). In contrast, the loss of widespread species on similar-sized islands increased β diversity (biotic heterogenisation). The distance between islands had no significant effects on the temporal changes in β diversity of birds. Our results reveal that the temporal β diversity of birds on fragmented islands was determined by both extinction and colonization, with the heterogenization caused by colonization of rare species being predominated. Thus, to further maintain or increase regional composition variation of birds in fragmented habitats, we could introduce suitable rare species from the regional pool on different islands. Our results highlight that the extinction-colonisation dynamics behind beta diversity are essential for understanding the spatiotemporal organisation of biodiversity.