Smoking considerably changes the oral microbiota vital for maintaining oral health; this possibly results in the development of diseases. Therefore, to restore the healthy oral microbiota, smoking cessation is a beneficial strategy. However, at present, the relationship between smoking cessation duration and oral microbial recovery remains unclear, and previous studies have not undertaken self-comparisons before and after smoking cessation. In the present study, we evaluated 30 healthy adult men with moderate-to-severe tobacco dependence who willingly quit smoking. Oropharyngeal swab samples were collected before and on day 30 of smoking cessation (experimental group). Simultaneously, samples were collected once from 30 never-smokers (control group). Metagenomic next-generation sequencing revealed differences in the β-diversity and relative abundance of the oral microbial species in both groups. Furthermore, linear discriminant effect size analysis identified the top 10 dominant species, which primarily belonged to the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. From before to day 30 after cessation, oropharyngeal microbiota composition gradually increased in the experimental group; thereafter, it gradually became similar to the composition in the control group. There is significant heterogeneity in the oral microbiota between smokers and never-smokers. A 30-day smoking cessation intervention can initiate a restorative trend in the oral microbiota of smokers.