BACKGROUND: The long-term impact of vitamin D deficiency and metabolic syndrome (MetS) on cardiovascular disease (CVD) and all-cause mortality are still a matter of debate. AIM: To test the hypotheses that lower serum 25 hydroxyvitamin D [25(OH)D] concentrations (a marker of vitamin D level) and MetS have a long-term impact on the risk of CVD and all-cause mortality, and individuals with vitamin D deficiency can be identified by multiple factors. METHODS: A sample of 9094 adults, 20 to 90 years of age, who participated in the Third National Health and Nutrition Examination Survey (NHANES III, 1988 to 1994) were followed through December 2015 was analyzed. The associations of serum 25(OH)D concentrations and MetS with CVD and all-cause mortality were analyzed longitudinally using Cox regression models. Classification and regression tree (CART) for machine learning was applied to classify individuals with vitamin D deficiency. RESULTS: Of 9094 participants, 30% had serum 25(OH)D concentrations < 20 ng/mL (defined as vitamin D deficiency), 39% had serum 25(OH)D concentrations between 20 to 29 ng/mL (insufficiency), and 31% had serum 25(OH)D concentrations ≥30 ng/mL (sufficiency). Prevalence of MetS was 28.4%. During a mean of 18 years follow-up, vitamin D deficiency and MetS were significantly associated with increased risk of CVD and all-cause mortality. Subjects with both vitamin D deficiency and MetS had the highest risk of CVD mortality (HR = 1.77, 95%CI: 1.22-2.58) and all-cause mortality (HR = 1.62, 95%CI: 1.26-2.09), followed by those with both vitamin D insufficiency and MetS for CVD mortality (HR = 1.59, 95%CI: 1.12-2.24), and all-cause mortality (HR = 1.41, 95%CI: 1.08-1.85). Meanwhile, vitamin D sufficiency significantly decreased the risk of CVD and all-cause mortality for those who even had MetS. Among the total study sample, CART analysis suggests that being non-Hispanic Black, having lower serum folate level, and being female were the first three predictors for those with serum 25(OH)D deficiency. CONCLUSION: Vitamin D deficiency and MetS were significantly associated with increased risk of CVD and all-cause mortality. There was a significant joint effect of vitamin D deficiency and MetS on the risk of mortality. Findings of the CART analysis may be useful to identify individuals positioned to benefit from interventions to reduce the risk of CVD and all-cause mortality.