As extensively used chemicals in a variety of consumer products, perfluoroalkyl substances (PFASs) are ubiquitous and could bring significant risk to human health. However, the effect of PFASs on metabolic syndrome (MetS) is not fully understood. In 2015, a preliminary cross-sectional study was undertaken. A total of 148 male subjects including 81 affected by MetS and 67 non–MetS participants as the reference were recruited from Physical Examination Center affiliated to Capital Medical University, China. Serum levels of perfluorohexane sulfonic acid (PFHxS), perfluorooctanoic acid (PFOA) and perfluorononanoic acid (PFNA) were significantly higher in the subjects with MetS. Logistic regression results showed that concentration of PFNA in serum was associated with 10.9–fold [95% confidence interval (CI), 2.00–59.1] increased risk of MetS. Moreover, increased serum PFNA concentrations were associated with high blood pressure [both for systolic and diastolic blood pressure (SBP and DBP); odds ratio (OR) 7.52 (95%CI, 1.34–42.1) for SBP and 7.27 (95%CI, 1.17–45.1) for DBP], hypertriglyceridemia [13.2 (95%CI, 2.34–74.2)] and obesity [13.3 (95%CI, 2.38–74.4)], respectively. After adjustment by age in logistic regression models, serum levels of PFOA were associated with 29.4–fold (95%CI, 2.90–299.7) increased risk of MetS. Increased PFOA levels were also correlated with MetS [29.4 (95%CI, 2.9–299.7)], SBP [10.8 (95%CI, 1.31–90.0)], hypertriglyceridemia [16.6 (95%CI, 1.92–147.1)], and obesity [46.7 (95%CI, 4.47–487.7)] with adjustment for age. This study suggests bodily retention of PFASs and its association with MetS. Further clinical and animal studies are warranted to clarify the putative causal relationship.