Only limited information is available on the inter-relationships between genetic and non-genetic factors such as diet and sunlight exposure with serum 25-hydroxyvitamin D [25(OH)D] concentration. This cross-sectional study aimed to examine the independent and interactive associations of season, dietary vitamin D intake, and SNPs of 11 vitamin D-related candidate genes with serum 25(OH)D concentration among 2,721 adults aged ≥40 years at baseline from the Yangpyeong cohort, a part of the Korean Genome Epidemiology Study (KoGES). The interactions between season or dietary vitamin D and 556 SNPs were evaluated using 2-degree of freedom joint tests. Season was strongly (pdifference = 1.00 × 10–12) and dietary vitamin D intake was slightly but significantly associated with serum 25(OH)D concentration (pdifference = 0.0119). Among five SNPs (rs11723621-GC, rs7041-GC, rs10500804-CYP2R1, rs7129781-CYP2R1, and rs2852853-DHCR7) identified in the screening steps, only one, rs10500804-CYP2R1, significantly interacted with season (pinteraction = 8.01 × 10–5). The inverse association between number of minor alleles of rs10500804-CYP2R1 and concentration of 25(OH)D was significant only in summer/fall. Conversely, dietary vitamin D intake was positively associated only in winter/spring. In conclusion, season, dietary vitamin D intake, and four SNPs in GC, CYP2R1, and DHCR7 are independently and rs10500804-CYP2R1 is interactively associated with serum 25(OH)D concentration. Serum 25(OH)D is influenced by genotype of rs10500804-CYP2R1 in summer/fall when sunlight exposure is high, while dietary vitamin D intake is an important determinant of serum 25(OH)D during the seasons with low cutaneous vitamin D synthesis.