The relationship between serum vitamin D levels and temporomandibular disorders (TMDs) remains unclear. Therefore, this study aimed to investigate the association between serum 25-hydroxyvitamin D (25[OH]D) levels and TMD incidence using large-scale health data. Clinical data from the electronic health records of six secondary or tertiary hospitals in Korea were used to evaluate the relationship between serum 25(OH)D levels and TMD incidence. The data were converted to the Observational Medical Outcomes Partnership Common Data Model. A cohort study was designed using the Cox proportional hazards model to examine the hazard ratio (HR) of TMD development after propensity score matching (PSM). An aggregate meta-analysis of the HR was subsequently performed. After 1:4 PSM, a target group with deficient 25(OH)D levels (<20 ng/mL) (N = 34,560) and comparator group with non-deficient 25(OH)D levels (≥20 ng/mL) (N = 47,359) were pooled from six hospital databases. HR meta-analysis demonstrated a significant association between deficient 25(OH)D levels and TMD incidence (pooled HR: 1.50; 95% confidence interval: 1.07–2.12). In conclusion, deficient 25(OH)D levels were found to be associated with an increased TMD risk. Therefore, vitamin D deficiency is a potential risk factor for TMD development.