Objective To explore the mechanisms of Qizhi Tongqiao capsule(QTC) in treatment of benign prostatic hyperplasia(BPH) and chronic prostatitis(CP) with the concept of "homotherapy for heteropathy" based on network pharmacology and molecular docking. Methods The active components and relevant targets of QTC were collected and obtained from TCMSP, BATMAN, PubChem, and Swiss Target Prediction database. Target genes of BPH/CP were predicted based upon GeneCards database. Intersectional targets were calculated by utilizing Venny 2.1.0. Cytoscape 3.10.1 was used to establish visual network diagram of "drug-ingredient-target-disease". Protein-protein interaction(PPI) network was constructed via STRING database and then input into Cytoscape for outputting key targets. Gene oncology (GO) function and kyoto encyclopedia of genes and genomes (KEGG) pathways enrichment analysis was conducted through Metascape database. Molecular docking was tested lastly. Results A total of seventy active components of QTC were obtained, quercetin, etc. included. There were 214 intersectional targets of "drug-disease". QTC could act in hypoxic and inflammatory micro-environment of prostatic tissue, upon several targets, such as HIF-1α, STAT3, IL-6 and so on, and regulate several relevant signaling pathways, such as NF-Κb, PI3K, HIF-1α and so on. Molecular docking indicated that quercetin had a good binding energy with all core targets. Conclusion QTC may act a "homotherapy for heteropathy" role in treating BPH and CP through ameliorating prostatic hypoxia and inflammation via various targets and signaling pathways. Nevertheless, much more studies should be further conducted to test and verify.