The nine hub genes (including TREM1, S100A9, FPR1, NCF2, FCER1G, CCR1, S100A12, MMP9, and IL1RN) were significantly upregulated, which may have a critical influence on the pathophysiological mechanism of PCOS and NAFLD. This evidence concerns the gene MMP9 and metabolic dysfunction-associated steatotic liver disease.