Small mammal assemblages were surveyed in five areas of the northern Junggar basin, Xinjiang, China, using standard trapping methods and index transects. In total, 23 species were recorded. The relationships between habitats and the distribution of the main species were described at local scale in Baihaba, Altai mountains. Three types of assemblages linked to (i) forest (Myodes rufocanus, Microtus agrestis, Myodes rutilus, Apodemus peninsulae, Sorex isodon), (ii) transitional areas and farmland ( mixed pool of species including Apodemus uralensis), and (iii) grassland (Ellobius tancrei, Microtus obscurus, Cricetulus migratorius) were identified. Additional species, such as Microtus oeconomus, could be found along small streams. At a broader scale, species composition was estimated in Kokehada, Narenhebuke and Fuhai areas and compared. Although ecological gradients from mountain grasslands to cold semi-desert partly explain differences in assemblage composition on a regional scale, similar habitats at the same altitude may, however, harbour different assemblages. For example, Spermophilus erythrogenys was the dominant species of the Kokehada grassland and Microtus obscurus and Ellobius tancrei were dominant in Baihaba grassland. In conclusion, the need for multi-scale standard descriptions of small mammal assemblage distribution in the northern Junggar basin of China is indicated