It is important to understand what genetic risk factors lead to hypertension and how genotype-specific dietary and lifestyle modification can mitigate the risk of developing hypertension. The ATP2B1 rs17249754 gene, which encodes a calcium pump expressed in vascular smooth muscle was identified as having variants that conferred higher or lower risk of hypertension—with the major allele carriers being increased at risk. However, the effects of dietary intakes on risk of hypertension among carriers of the different alleles have not been fully elucidated. Therefore, we evaluated ATP2B1 rs17249754 and its interaction with dietary intakes of sodium (Na), potassium (K) and calcium (Ca) on the risk of developing hypertension using the Ansan/Ansung (n = 8842) and City-Rural (n = 5512) cohorts from the Korean Genome and Epidemiology Study. Carriers of the major allele of ATP2B1 rs17249754 were at greater risk of developing hypertension and high Na intake and low Ca increased the risk more in major allele than among minor allele carriers. High potassium intake was more protective against hypertension in the subjects expressing minor alleles and a low Na/K intake ratio was the most consistently beneficial to the subjects expressing the minor allele. When controlling for Na and K, low Ca intake was associated with a substantially higher risk for high systolic blood pressure in the major allele carriers compared with minor allele, suggesting good calcium status is especially important for the major allele carriers. In conclusion, people with the major allele of ATP2B1 rs17249754 are susceptible to hypertension especially in low intake of Ca and high ratio of Na and K.