Zhuang Medicine Jin-mu Granules (ZMJG) are prescriptions derived from the Zhuang nationality, which is the largest minority among 56 ethnic groups in China. They have been widely used in the treatment of chronic pelvic inflammatory disease (CPID) in Guangxi Zhuang Autonomous Region for clearing away heat and toxins, removing dampness and poisoning. CPID is a common gynecological disease of female reproductive organs and surrounding tissues and is characterized by persistent and recurrent symptoms, causing serious physical and psychological damage to the patient. Preliminary research found that ZMJG have beneficial effects on CPID model rats, but the metabolic mechanism underlying their protective effects is unclear. In this study, we used the strategy of combining network pharmacology, pharmacodynamic, and metabolomic approaches to investigate the molecular mechanisms and potential targets of ZMJG for the treatment of CPID. First, a network diagram of “medicinal materials-components-targets-pathways” based on network pharmacology was constructed to obtain a preliminary understanding of the biologically active compounds and related targets of ZMJG and clarify their molecular mechanism in CPID. Subsequently, the in vivo efficacy of ZMJG was verified in a rat model. Furthermore, we analyzed the corresponding metabolomics profile to explore the differentially induced metabolic markers and elucidate the metabolic mechanism by which ZMJG treat CPID. The results show that the therapeutic effect of ZMJG on CPID is mediated through multiple pathways, metabolic pathways, and multi-component multi-target modes, providing a detailed theoretical basis for the development and clinical application of ZMJG and a new research idea for the treatment of CPID in Chinese medicine.