Small mammal species may utilise different vertical strata of vegetation, and environmental characteristics may influence this utilisation. Consequently, microhabitats can provide important information regarding their role in space use. This study aimed to evaluate whether habitat structure influences the spatial use of small mammals in Sergipe, northeastern Brazil. Fieldwork was conducted monthly between August/2022 and July/2023 in the Atlantic Forest area. A total of 120 Sherman traps were baited on the ground and understory, resulting in a sampling effort of 4,320 trap-nights. Microhabitat characteristics were recorded at each capture station every three months. The Pianka index was used to check for niche overlaps, and Canonical Correspondence Analysis (CCA) was applied to evaluate associations between species and habitat variables. The marsupial Marmosa demerarae and the rodent Cerradomys vivoi significantly utilised the understory, and Marmosops incanus was found on the ground. The marsupial Didelphis albiventris did not differ in its occurrence between strata. When all four species were analysed together, the null model indicated spatial resource partitioning. The CCA explained 46% of the total variation in species captured by habitat variables, with only litter depth being significant for the capture of C. vivoi. This species and M. incanus showed changes in their patterns of vertical stratum use, which may be related to the type of local phytophysiognomy present. Spatial segregation is an important factor that facilitates species coexistence. Locations with greater litter depths can provide shelter for C. vivoi, reducing the chances of detection by predators and benefiting from the consumption of invertebrates in the litter. Therefore, the distribution of species according to vertical stratification in the environment, as well as spatial segregation that can minimise interspecific competition, are important components in structuring the small-mammal community.