Vaginal intraepithelial neoplasia (VAIN) is a precancerous condition with significant potential for malignant transformation. The 5-aminolevulinic acid photodynamic therapy (ALA-PDT) is considered as a novel approach to treat VAIN. Recent studies have shown that an imbalance in the vaginal microbiota can affect the progression of VAIN. Thus, the effect of imbalanced microbiota on the efficacy of ALA-PDT for treating VAIN needs to be determined. Sixty-five female patients diagnosed with VAIN were recruited. 5-aminolevulinic acid was applied topically to the vaginal wall, followed by 635 nm red light at intervals of 7-14 days. Cytological inspections, high risk human papillomavirus (HR-HPV) genotyping, vaginal colposcopy examinations, histopathology and culture and identification of vaginal microflora were performed before and after treatment. Among the 62 patients, the complete remission rate (CRR) of vaginal wall lesions was 85.5 %, and the HR-HPV clearance rate was 61.3 %. In the balanced vaginal microbiota group, the CRR of vaginal wall lesions reached 97.2 %, with an HR-HPV clearance rate of 75.1 %. In the imbalanced vaginal microbiota group, the CRR of vaginal wall lesions was only 65.5 %, with an HR-HPV clearance rate of 48.3 %. There was a trend of improved clearance of lesions and HR-HPV when the vaginal microbiota was balanced (p= 0.002 and p= 0.038, respectively). During the process of clinical treatment and the 1-year follow-up period, all patients experienced minimal adverse reactions. The findings of this study demonstrate that ALA-PDT is a clinically effective and safe treatment for VAIN, and the vaginal microbiota's status is a key factor affecting the efficacy of ALA-PDT for VAIN.