Abstract： Objective： To analyze the molecular mechanisms of Sanwu Huangqin Decoction in the treatment of pelvic inflammatory disease （PID） and prostatitis with homotherapy for heteropathy. Methods： The main active components and targets of Sanwu Huangqin Decoction were screened using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform （TCMSP） ， HERB database， PubChem database， and SwissTargetPrediction database. Related targets of PID and prostatitis were obtained from GeneCards and OMIM databases， and the intersection was taken to obtain common targets between the medicinals and diseases. The intersection targets were imported into the STRING database to construct a protein-protein interaction （PPI） network， and Cytoscape 3.10.0 software was used for visualization and to identify key targets. Gene Ontology （GO） functional analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analysis of the targets were performed using the DAVID database， and an active component-intersection target-pathway network diagram was constructed. Molecular docking validation was conducted for key targets and main active components. Results：A total of 58 active components and 427 targets of Sanwu Huangqin Decoction were screened from the databases. After intersection analysis with PID and prostatitis，97 intersection targets were obtained. Using the Network Analyzer plugin，core components such as quercetin and β-sitosterol，and core targets such as protein kinase B1（ AKT1），B-cell lymphoma 2（ BCL2）， and signal transducer and activator of transcription 3 （STAT3） were identified. GO functional analysis enriched 811 entries related to gene expression， and KEGG analysis enriched 96 pathways， including tumor necrosis factor （TNF） and mitogen-activated protein kinase （MAPK）. Molecular docking showed that key targets （AKT1， BCL2， and STAT3） could freely bind with main active components （quercetin， β-sitosterol）， with the strongest binding activity between quercetin and STAT3. Conclusion：Components such as quercetin and β-sitosterol in Sanwu Huangqin Decoction act on targets like AKT1，BCL2，and STAT3，regulating pathways such as the TNF and MAPK pathways，to exert therapeutic effects on PID and prostatitis with homotherapy for heteropathy.