Polycyclic aromatic hydrocarbon (PAH)-contaminated soils are usually complex and characterized by a lack of nutrition and soil salinization, resulting in difficulties in soil remediation. In this study, bioaugmentation with a PAH-degrading Bacillus PheN7 (BA) and low-dose persulfate oxidation (PS), along with natural biodegradation, were utilized to remediate alkaline PAH-contaminated soil. The soil used in the study had a pH of 9.35, and the total PAH content was 568.8 ± 31.0 mg/kg dry soil. After 42 d of remediation, the degradation efficiency of PAHs was 96.72% and 93.88% using persulfate oxidation and bioaugmentation, respectively, whereas 38.66% of PAHs were degraded in natural attenuation (NA). Bacillus was the dominant genera throughout the process of bioremediation with the relative abundance of 79.3% on day 42 in the BA system, whereas, Alcanivorax was enriched and became the dominant genera in PS systems. In the meantime, PAH degradation genes were detected with remarkably higher level in the BA system than in PS system during the remediation. In addition to the degradation of contaminants, persulfate oxidation promotes microbial bioremediation efficiency mainly by lowering the pH to neutral and increasing the active phosphorus content in the soil. Microbial species and ecological niches were less reduced in the PS system than in the BA system. Collectively, persulfate oxidation had a better impact on the soil microbiome and is more suitable for long-term soil health than bioaugmentation through PheN7 addition.