The change and mechanism of soil and soil bacterial diversity during the change of herbaceous litter thickness in desert areas is crucial to understand. In the study, the dominant herbaceous litter mixture in Baijitan National Nature Reserve was selected as the research material, and an experiment was established by adjusting the litter depth. The results showed that the measured values of soil physicochemical factors (total nitrogen, total protein, total potassium, available phosphorus, available potassium, pH, and soil water content) increased with the increase of herbaceous litter mixture thickness in 0–5 cm soil layer. Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the dominant bacterial phyla under different thicknesses of herbaceous litter in 0–5 and 5–10 cm soil layers. Balneimonas, Rubrobacter, and Geodermatophilus were the dominant bacterial genera under different thicknesses of herbaceous litter in 0–5 and 5–10 cm soil layers. There was no obvious change in the α-diversity index of bacterial community the same soil layer, but the α-diversity index in the 0–5 cm soil layer was lower compared to the 5–10 cm soil layer. The results of this study revealed that the change of herbaceous litter thickness had no significant effect on soil bacterial community structure in desert areas.