Introduction 25-Hydroxy vitamin D (Vit D3) deficiency was found to be associated with vascular dysfunction, arterial stiffening, extent of coronary artery disease and cardiovascular mortality. Previous studies showed positive correlation between serum Vit D3 and HDL-C and negative correlation between Vit D3 and LDL-C. The aim of this study is to investigate more details about the possible association of serum Vit D3 level with lipid, lipoprotein and apolipoprotein level. Methods Totally 101 patients were included in this study and Vit D3, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), High-density lipoprotein cholesterol (HDL-C), total triglyceride (TG), non-high-density lipoprotein cholesterol (Non-HDL-C), low-density lipoprotein particle (LDL-P), small dense low-density lipoprotein particle (sLDL-P), small dense low-density lipoprotein cholesterol (sdLDL-C), High-density lipoprotein cholesterol particles (HDL-P), High-density lipoprotein 2-cholesterol (HDL2-C), Apolipoprotein B(ApoB), Apolipoprotein A1 (Apo A1) and Apolipoprotein B/Apolipoprotein A1 ratio (ApoB/A ratio) were tested. Results Our results show that patients with Vit D3 deficiency (Vit D3 < 30 ng/ml) have significantly higher level of LDL-C, TG, Non-HDL-C, LDL-P, sLDL-P, sdLDL-C, ApoB and ApoB/A ratio compare with patients have normal Vit D3 level (Vit D3 > 30 ng/ml). Patients with normal Vit D3 level have significantly higher level of HDL-C and HDL2-C. Correlation study shows that Vit D3 level is negative correlated with TC, LDL-C, TG, Non-HDL-C, LDL-P, sLDL-P, sdLDL-C, ApoB and ApoB/A ratio and positive correlated with HDL2-C level. Conclusion Our results show that Vit D3 deficiency links to an increased risk for dyslipidemia and that may be the reason that patients with vitamin D deficiency tend to have higher risk of coronary artery disease.