The Sichuan Heizhugou National Nature Reserve is located in the Liangshan Mountains, which is highly rich in biodiversity and plays an important role in protecting and maintaining the regional biodiversity. However, there is a lack of mammalian research in the nature reserve. In order to understand the small mammal communities of the nature reserve and its surroundings, from April to October 2018, we investigated the species diversity and community composition of non-volant small mammals in the region. A total of 184 quadrats including 9,016 traps were set along an elevational gradient from 1,537-3,830 m. We captured small mammal individuals (N = 536), which belong to 4 orders, 7 families, 13 genera, and 21 species. Nine species, including Vernaya fulva and Uropsilus aequodonenia, had been reported for the first time in this region, enriching the species distribution records. According to historical data and our survey, there are a total of 43 species of small mammals, belonging to 4 orders, 9 families and 28 genera in the Heizhugou region. Of the 43 small mammal species, 37 (86%) species are of Oriental origin, and 18 (48.6%) species are of Himalayan-Hengduan Mountains origin. For the 21 small mammal species captured, the dominant species were Apodemus draco (33.2%), Niviventer confucianus (21.3%), and Eothenomys chinensis (12.7%). Along the elevational gradient, the community composition changed from a Niviventer confucianus + Apodemus draco + Niviventer fulvescens + Anourosorex squamipes dominated community to a Eothenomys chinensis + Apodemus draco + Proedromys liangshanensis + Eothenomys custos dominated community. The proportion of Himalayan-Hengduan Mountains origin species increased with elevation. The average lower limit, mid-point, and upper limit of elevation for endemic species mainly distributed in the Himalayan-Hengduan Mountains were higher than that of non-endemic species. The average mid-point and lower limit of elevation of endemic species was significantly higher than that of non-endemic species (n = 21, df = 19, P = 0.013; n = 21, df = 19, P < 0.01). Species composition in this region is mainly represented by fauna of Oriental origin, while the middle and high elevational communities are mainly composed of endemic species. This study enriched the previous species diversity and distribution records of the small mammals, which is important for the study and conservation of species diversity in this region.