Naphthalene is a biocide of soil fauna, particularly of soil arthropods, that has been widely applied to test the functional roles of soil fauna in soil processes. However, whether the use of naphthalene to expel soil fauna has a non-target effect on soil bacteria in subalpine forests remains unclear. We conducted a naphthalene treatment experiment to explore the effects of naphthalene on the soil bacterial community in subalpine forest soil. The results suggested that naphthalene treatment (at 100 g.m-2 per month) significantly increased the abundances of total bacterial, gram-positive bacterial and gram-negative bacterial phospholipid fatty acids (PLFA) and did not change the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) or MBC/MBN ratio. Moreover, a total of 1038 operational taxonomic units (OTUs) were detected by Illumina MiSeq sequencing analysis. Proteobacteria, Actinobacteria, and Acidobacteria Chloroflexi were the dominant phyla, and Bradyrhizobium was the most abundant genus. The naphthalene treatment did not affect soil bacterial diversity or community structure. Overall, these results demonstrated that the naphthalene treatment had non-target effects on the active bacterial community abundance but not the soil bacterial community structure. Thus, the non-target effects of naphthalene treatment should be considered before using it to expel soil fauna.