Congenital heart diseases (CHDs) are the most common birth defects and the leading cause of non-infectious deaths in infants, with an unknown etiology. We aimed to assess the association of genetic variations in UCP2 gene, dietary factors, and their interactions with the risk of CHDs in offspring. The hospital-based case-control study included 464 mothers of children with CHDs and 504 mothers of healthy children. The exposures of interest were maternal dietary factors in early pregnancy and UCP2 genetic variants. Logistic regression analyses were used to assess the association and interaction of UCP2 gene and dietary factors with CHDs. Our results found that the polymorphisms of UCP2 gene at rs659366 and rs660339, together with maternal dietary factors including excessive intake of pickled vegetables and smoked foods were associated with increased risks of CHDs in offspring. Regular intake of fresh meat, fish and shrimp, and milk products were associated with lower risks of CHDs in offspring. Besides, positive interaction between the dominant model of rs659366 and excessive intake of pickled vegetables was found in the additive interaction model (RERI = 1.19, P = 0.044). These findings provide the theoretical basis for gene screening and a new clue for the prevention of CHDs in offspring.