Oceanic island ecosystems are highly vulnerable to human activities. Furthermore, oceanic islands near the mainland offer unique insights into natural processes, including overseas dispersal from the mainland. However, most studies examining community changes on oceanic islands focus on human activities, while natural colonisation from the mainland has received limited attention. To clarify the mechanisms of insular community changes due to human activities and natural colonisation, we investigated bird assemblages on ten islands during 2016 and 2021 and compared them to the assemblages during 1970 and 1973 on the Izu Islands, Japan. The effects of mainland distribution changes and species traits on the colonisation and disappearance of bird species on the islands were examined using phylogenetic generalised least squares (PGLS) models. Bird community structures on each island were examined based on species richness and functional and phylogenetic structures. A null modelling approach was used to examine functional and phylogenetic cluster/overdispersion structures; clustering and overdispersion imply environmental filtering and limiting similarity, respectively. The effects of geographical and topographical characteristics, weasel introduction, and landscape transformation were examined using linear models (LMs). Species with expanded mainland distribution and large clutches colonised more islands than the other species. Raptors disappeared from many islands. Species richness decreased, and functional and phylogenetic structures clustered on almost all islands, which were only statistically associated with geographical and topographical characteristics. The distribution changes of species on islands were associated with their mainland distribution changes, which indicates that mainland community dynamics influence insular communities via overseas dispersal. Despite colonisations of species from the mainland, the net loss of species richness, clustered phylogenetic and functional structures, and disappearance of top-predators on many islands suggest that bird communities across the archipelago degraded. Furthermore, previous studies have demonstrated that introduced weasels negatively affect birds through competition for food resources and direct predation on the introduced islands. These degraded bird communities due to introduced weasels would have transboundary biodiversity effects on communities across the archipelago via inter-island movements of birds, which suggests the need for comprehensive conservation strategies across the archipelago to effectively conserve insular biodiversity.