Oasis habitats play a critical role in arid areas, yet little is known regarding microbial community assembly processes and their divergence between oasis and desert habitats in arid inland river basins. Herein, using 21 and 18 sample data points collected from oasis and desert habitats, respectively, in the lower reaches of the Heihe River (Northwest China), we examined the assembly processes of soil bacterial and fungal communities and identified drivers governing the balance between deterministic and stochastic processes. We found that deterministic processes (particularly variable selection) dominated bacterial community assembly in oasis habitat, while stochastic processes were more important in the desert habitat. In contrast, stochastic processes dominated fungal community assembly in both habitats, with dispersal limitation playing a predominant role. Environmental factors (e.g., soil electrical conductivity) and microbial species associations significantly mediated bacterial community assembly, where high electrical conductivity level promoted stochastic processes while low electrical conductivity enhanced deterministic processes. However, both environmental and species associations had little/no effects on fungal community assembly. These results highlight that soil microbial community assembly processes and their underlying drivers are habitat-and taxon-dependent at small scale arid inland river basins.