Understanding the process underlying the spatial gradients in biodiversity is a fundamental issue in ecology. Altitudinal gradients are ideal systems for examining the community assembly process because they represent rapid changes in environmental conditions over relatively short distances. The functional and phylogenetic approaches allow a deeper mechanistic understanding of the underlying assembly process. However, whether community assembly from montane to alpine zones is driven more by ecological constraints or human settlement patterns is not fully resolved and may vary by system. Here, we examined the phylogenetic and trait-based functional structures from the montane to alpine zones and clarified the effects of natural environmental factors and human-induced landscape transformation on the breeding bird assemblage on Mount Norikura, central Japan. Breeding birds from 700 to 3026 m a.s.l. were surveyed in 2016–2017. Bird community structures were examined based on species richness, functional and phylogenetic structures. A null modelling approach was performed to examine functional and phylogenetic cluster/overdispersion structures; clustering and overdispersion imply species elimination by environmental filters and limiting similarity as a corollary of competitive exclusion of species, respectively. Furthermore, we examined the relative effect of natural environments and human disturbance. Bird species richness was high in the mountain base to mid-elevation, then decreased with elevation. We found a contrasting pattern in the phylogenetic and functional structures in the alpine zone: phylogenetic overdispersion and functional clustering. In contrast, the functional and phylogenetic structures were clustered in the upper parts of the subalpine zone. The functional and phylogenetic clusterings in the lower parts of the subalpine and montane zones were negligible with the weak effects of the environmental filtering. Single-trait analysis showed that the high abiotic tolerance and foraging or nesting capabilities in treeless environments were clustered in the alpine zone, and mobility was clustered in the subalpine zones. Natural environments strongly affected bird community structures, but human disturbance added species to assemblages in the mountain base to mid-elevation and changed the functional and phylogenetic structures. Our findings highlight that filtering by severe natural environments is a fundamental community assembly process in high mountain regions, whereas filtering effects can be weaker at lower elevations. Furthermore, the filtering effect should differ between the alpine and the upper parts of the subalpine zones because of different combinations of clustered traits. Climate change and landscape transformation pressures may strongly impact biodiversity in the alpine and subalpine zones, respectively.