To investigate the mechanism by Ba-Duan-Jin in the treatment of fibromyalgia. Twenty eligible fibromyalgia patients were selected, and were trained and guided online by an experienced Ba-Duan-Jin instructor with reference to the standard operating procedure (SOP) for a 12-week course of 1 hour twice a week. The evaluation points were 0, 4, 8, and 12 weeks. The change of pain Visual Analogue Score (VAS) and tener point count (TPC) post-treatment were evaluated. And blood, feces, and brain fMRI were collected from the patients at 0 and 12 weeks to compare the changes in gut microbiota, metabolites, and brain function networks before and after the intervention with the 16SrRNA sequencing, targeted metabolomics, and real-time Quantitative Polymerase Chain Reaction (PCR).