ETHNOPHARMACOLOGICAL RELEVANCE: Polygonum capitatum Buch.-Ham. ex D. Don (Pc, DB52/YC141-2003), a traditional herbal medicine utilized by the Miao nationality, is acknowledged for its therapeutic potential and efficacy in treating various urologic disorders, notably chronic bacterial prostatitis (CBP). Experimental and clinical studies have demonstrated that the combination of Pc with Ciprofloxacin (CIP) effectively alleviates the urinary symptoms in CBP patients, offering superior outcomes compared to monotherapy. However, the underlying mechanisms and specific constituents responsible for this synergistic effect remain poorly understood, which hinders its broader clinical application. AIM OF THE STUDY: This study aims to elucidate the potential synergistic mechanism of Pc and CIP in ameliorating CBP and to identify the major active ingredient of Pc that contributed most significantly to the therapeutic efficacy when combined with CIP. MATERIALS AND METHODS: A rat model of CBP was induced in rats by prostate bilateral injections of Escherichia coli (E. coli.), followed by therapeutic intervention with a combination of Pc and CIP. The therapeutic effect of this combination was assessed by quantifying the Prostate viscera coefficient (PVC) and bacterial colonization. Histopathological changes in the prostate were observed using HE staining. The expressions of inflammatory mediators was quantified using Western blotting (WB), qRT-PCR, and immunohistochemical staining (IHC). To elucidate the molecular mechanisms underlying the synergism of the combination therapy, transcriptomic profiling was performed using RNA sequencing (RNA-seq). Differentially expressed genes were analyzed via Ingenuity Pathway Analysis (IPA) to identify regulated pathways, with critical targets further validated by qRT-PCR and WB. For direct drug target identification, Tissue-thermal proteome profiling (Tissue-TPP) was implemented, incorporating differential temperature heat treatment, data-independent acquisition (DIA) quantitative proteomics, and thermal shift curve analysis to characterize interaction targets of the Pc-CIP combination in prostate tissue. Binding affinity between the drug combination and identified targets was further confirmed through thermal shift assays. Finally, molecular docking simulations were conducted to characterize the predominant bioactive constituents of Pc that contributed synergistically to therapeutic outcomes when co-administered with CIP. RESULTS: The results indicated that the combination of Pc and CIP significantly reduced the PVC and bacterial concentration, restored the prostate gland structure, and inhibited the mRNA and protein expression of pro-inflammatory factors (TNF-α and IL-1β) in CBP rats. RNA-Seq combined with IPA analysis showed that Pc combined with CIP significantly inhibited inflammatory signaling pathway in CBP rats, especially the NF-κB/IL-6/JAK2/STAT3 pathway. Moreover, Tissue-TPP revealed that Pik3cb is a direct target of Pc combined with CIP. Molecular docking studies showed that GA, a predominant component of Pc, can directly bind to Pik3cb. Finally, it was also found that the combination of GA and CIP significantly improved CBP. CONCLUSION: The results suggest that Pc combined with CIP can mitigate CBP by targeting Pik3cb to inhibit the NF-κB/IL-6/JAK2/STAT3 signaling pathway, and GA may be a potential pharmacodynamic substance of Pc.