This study aimed to analyze the characteristics of soil microbial communities of Hippophae rhamnoides forest during the revegetation of abandoned cropland in the Loess Plateau in China. We used high-throughput sequencing technology to analyze the carbon (C) and nitrogen (N) characteristics of soil microorganisms and the relationship between the soil environment and the soil microbial community structure in pure and mixed Hippophae rhamnoides forests in Wuqi County, Shaanxi province. The findings revealed that soil microbial C and N in different soil layers showed a decreasing trend with an increase in soil layers and the structural difference of the soil microbial community among different forest stands in the study area was smaller than that among different soil layers. Gracilibacteria, Gemmatimonadetes, Nitrospirae, Parcubacteria, and Actinonobacteria in bacteria were significantly correlated with soil environmental factors. Ichthyosporea and Ciliophora in fungi were strongly affected by environmental factors. The effect of environmental factors on bacteria is greater than that on fungi. Our findings can provide some data to support and feasible suggestions for studies on revegetation in the Loess Plateau.