Objective Existing evidence suggests that vitamin D deficiency may contribute to the development of atherosclerosis. The aim of our cross-sectional study was to assess the association of circulating vitamin D metabolite concentrations with insulin resistance and subclinical atherosclerosis in patients with T2DM. Methods One hundred twenty T2DM patients who were measured serum 25-hydroxyvitamin D (25(OH)D) at diabetes clinic, from January 2013 to June 2013 (53 males and 67 females, mean age 58 years, mean duration of DM 6.8 years) were enrolled. Carotid atherosclerosis and abdominal visceral fat thickness were assessed by B-mode ultrasonography. In addition, the patients were evaluated diabetic microangiopathies and brachial-ankle pulse wave velocity (baPWV) and ankle-brachial index (ABI) to evaluate atherosclerotic burden. Results The prevalence of deficiency (< 10 ng/mL) and sufficiency (≥ 30 ng/mL) of vitamin D in T2DM patients was 28.3% and 8.3%, respectively. The group of patients with lowest quartile of 25(OH)D showed significantly higher carotid IMT than those other quartiles (P = 0.018). And the group with lowest quartile of 25(OH)D showed significantly lower visceral fat thickness than other groups (P = 0.01). Serum 25(OH)D levels were positively related with visceral fat thickness (r = 0.292, P = 0.019). However, no 25(OH)D was associated with either HOMA-IR levels representing insulin resistance or baPWV. There was no significant difference in prevalence of diabetic microangiopathies such as retinopathy, nephropathy and neuropathy between groups. Conclusion In this present study, low 25(OH)D levels were associated with increased subclinical carotid atherosclerosis and lower visceral adiposity.