Diversity can be partitioned into several components and dimensions that are affected in different ways by habitat loss and fragmentation. However, these partitions and dimensions are rarely investigated in human-modified landscapes. In this study, we investigated different partitions (Hill numbers) and dimensions (taxonomic [TβD], functional [FβD] and phylogenetic [PβD]) of small mammal β-diversity in a fragmented landscape of central Brazil using a multi-scale approach. TβD was estimated considering rare, common and abundant species. Tolerance to disturbed habitat, assessed via the traits “habitat use”, “tail length” and “use of vertical strata”, and trophic guild, defined by “diet”, were used to estimate FβD. PβD was based on phylogenetic relatedness of the sampled species. The association between different partitions and dimensions of β-diversity and habitat and landscape attributes was investigated using Mantel tests. We found a significant positive effect of geographical distance on all partitions and dimensions of β-diversity. Canopy cover were positively associated with abundance-based TβD, FβD and PβD. While, forest area and normalized difference vegetation index (NDVI) were associated with PβD and FβD, respectively. Our findings support the hypothesis that even in a highly modified landscape, small mammal’s β-diversity is determined by different environmental factors and geographical distance of forest patches. However, the relatively higher importance of distance appears to be related to dispersal limitation of this group.