Our objective is to determine circulating Bone morphogenetic protein-9(BMP-9) levels in subjects with Metabolic Syndrome (MetS) and examine the relationship between BMP-9 and conventional markers for MetS and insulin resistance (IR). A total of 362 newly diagnosed patients with MetS along with healthy controls were recruited for this cross-sectional study. Circulating BMP-9 levels were measured by ELISA. Circulating BMP-9 levels were significantly lower in MetS patients compared to those of the healthy controls. BMP-9 was associated negatively with Waist hip ratio (WHR), fasting blood glucose (FBG), 2-hour blood glucose after glucose overload (2h-OGTT), HbA1c, triglyceride (TG) levels and HOMA-IR and positively with free fatty acid (FFA) and HDL after control for age and sex. In a multiple linear regression, BMP-9 was independently associated with type 2 diabetes mellitus (T2DM), HOMA-IR and FFA. Binary logistic regression showed that plasma BMP-9 concentrations were significantly associated with MetS even after controlling for anthropometric variables and lipid profiles. In addition, circulating BMP-9 levels reduced progressively with an increasing number of MetS components. The best cutoff values for circulating BMP-9 to predict MetS was 56.6 ng/L. Circulating BMP-9 levels were associated with the key components of MetS and IR.