A growing body of literature has documented that job stress is associated with the development of cardiovascular disease. Nevertheless, the pathophysiological mechanism of this association remains unclear. The purpose of this study is to elucidate the relationship between job stress, heart rate variability, and metabolic syndrome. The study design was cross-sectional, and a total of 169 industrial workers were recruited. A structured-questionnaire was used to assess the general characteristics and job characteristics (work demand, decision latitude). Heart rate variability (HRV) was recorded using SA-2000 (medi-core), and was assessed by time-domain and by frequency-domain analyses. Time domain analysis was performed using SDNN (Standard Deviation of normal to normal interval), and spectral analysis using low-frequency (LF), high-frequency (HF), and total frequency power. Metabolic syndrome was defined on the basis of risk factors being clustered when three or more of the following cardiovascular risk factors were included in the fifth quintile: glucose, systolic blood pressure, high-density lipoprotein cholesterol (bottom quintile), triglyceride, and waist-hip ratio. The results showed that job characteristics were not associated with cardiovascular risk factors. Compared to the lower strain group (low strain+passive+active group), the high strain group had a less favorable cardiovascular risk profile with higher levels of blood pressure, glucose, homocysteine, and clotting factor, but the difference was not statistically significant. The SDNN of HRV was significantly lower in the high strain group than in the low strain group. The prevalence of metabolic syndrome in the lower strain group and high strain group was 13.2% and 23.8%, respectively. In the high strain group, the metabolic syndrome was significantly related to a decreased SDNN. However, we could not find a significant association in LF/HF ratio. This result suggests that decreased HRV found in the high-strain group are not a direct indicator of disease. However, it can induce cardiovascular abnormalities or dysfunctions related to the onset of heart disease among high risk groups.