Although desert reclamation efforts have been used for increased crop production, their impacts on the structure of soil microbial communities remain largely understudied. Here, six adjacent pairs of different native desert and newly reclaimed cropland soils across a 3300 km transect in northern China were selected to address how microbial biomass, community composition, biogeographic pattern and the relative importance of ecological processes responded to agricultural reclamation using qPCR and high-throughput amplicon sequencing of bacterial 16S rRNA and fungal ITS genes. Agricultural intensification generally increased bacterial and fungal biomasses compared to undisturbed desert soils, while most microbial α-diversities were not significantly changed across these sampling sites. The relative abundances of some dominant microbial phyla and families significantly changed in response to agricultural intensification, which was site-dependent. Bacterial and fungal communities showed similar biogeographic patterns predominantly dominated by community turnover rather than nestedness for both desert and cropland soils, while agricultural intensification made bacterial community compositions more dissimilar. Deterministic process and stochastic process dominated bacterial and fungal community assembly in both desert and cropland soils, respectively. Agricultural intensification slightly reduced the relative importance of deterministic process for bacterial community assembly, while it conversely increased the relative importance of deterministic process to fungal community assembly by shifting the contributions of different assembly components. These results suggest that short-term land-use transformation from native deserts to croplands impact desert soil microbial community structure by making bacterial community more stochastic and fungal community more deterministic.