Plasma cell mastitis (PCM), a chronic breast inflammatory disease, is characterized by ductal dilatation and plasma cell infiltration. Traditional Chinese Medicine (TCM) Yanghe decoction is used to relieve mastitis symptoms clinically. However, its efficacy and mechanism on PCM remain undefined. The PCM patients receiving dexamethasone and metronidazole tablets, served as control group, with the other group receiving combination of Yanghe decoction, 15 cases each. Main symptom indicators included mass size, skin colour, skin temperature, breast pain, blood cell count (WBC), C reactive protein (CRP), interleukin (IL)-6, IL-4, serum prolactin (PRL), erythrocyte sedimentation rate (ESR), immunoglobulin A (IgA), IgM, and IgG levels. Secondary indicators included TCM syndrome and anxiety/depression scores. Breast differential flora (DF) and metabolites (DAMs) post-treatment between two groups were detected by 16S rRNA sequencing and metabolomics, with further correlation analysis. Post-treatment symptom scores exhibited lower than pre-treatment in both groups, with greater decline on WBC, CRP, IL-6, IL-4, PRL, and ESR, and enhanced IgA, IgM, and IgG levels in Yanghe decoction group than in control group. Notably, Yanghe decoction group demonstrated no significant DF, with decreased Corynebacterium and Rhodococcus, and elevated Staphylococcus, which correlated significantly with the above indicators. Moreover, 43 DAMs were detected between these two groups, with Glycerophosphocholine, 9,10-Epoxyoctadecenoic acid, Arachidic acid, and 4,5-Dihydroorotic acid showing strong correlations with the above flora. Based on the clarification of PCM improvement with Yanghe decoction, we preliminarily explored potential roles of breast tissue microorganisms and DAMs, providing scientific basis for its clinical application and potential clinical biomarkers in PCM.