Vitamin D deficiency (VDD) is common in women with and without polycystic ovary syndrome (PCOS) and may be associated with metabolic and endocrine disorders in PCOS. Aim of the study was to evaluate the association between serum vitamin D level and metabolic syndrome (MS) in PCOS. This cross-sectional study was conducted in PCOS clinic of infertility outpatient department of the department of Reproductive Endocrinology and Infertility at Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from July 2018 to June 2019. A total of 170 diagnosed patients with PCOS of aging 20 to 40 years were included in this study. Out of which 85 patients with PCOS MS and rest 85 patients without PCOS MS were considered as Group I and Group II respectively. Serum vitamin D was measured using a chemiluminescent microparticle immunoassay (CMIA). Almost two third (72.9%) populations had vitamin D moderate deficiency (10-20ng/ml) in Group I and 46(54.1%) in Group II. The mean vitamin D was 13.97±4.53ng/ml in Group I 16.02±6.62ng/ml in Group II. There were significant negative correlation found between vitamin D level with weight (r = -0.169; p=0.028), waist circumference (r = -0.208; p=0.007), Waist/Hip ratio (r = -0.205; p=0.007) and diastolic blood pressure (r = -0.187; p=0.014). In binary logistic regression analysis diastolic blood pressure (OR=1.04, 95% CI 0.89-1.29), fasting Glucose (OR=1.09, 95% CI 0.89 - 1.42), HDL (OR=1.11, 95% CI 1.05 - 1.17) and Vitamin D (OR=1.37, 95% CI 1.01 - 1.82) were significant risk factors of metabolic syndrome of the study patients. Vitamin D level was lower in PCOS subjects having MS and higher frequency of body weight, vitamin D deficiency was observed in them compared to the non-MS group. Waist: hip ratio, waist circumference and diastolic blood pressure were the negatively correlated with of vitamin D in the study subjects.