This study first reveals acetate as a key gut microbiota metabolite to ameliorate endometriosis (EMs) via JAK1/STAT3‐mediated M1 macrophage polarisation, confirming healthy donor faecal microbiota transplantation (FMT) improves EMs by reshaping microbiota, enhancing acetate, strengthening intestinal barriers and providing a new therapeutic paradigm. Here, STAT3 is linked to endometriosis.