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This study aimed to explore the association of maternal diet, infant <i>MTHFR</i> gene polymorphisms, and their interactions with the risk of ventricular septal defects (VSDs). This case–control study recruited 448 mothers of VSD children and 620 mothers of healthy counterparts. Multivariable-adjusted logistic regression models were constructed to examine the association between maternal dietary habits during the first trimester of gestation, <i>MTHFR</i> gene polymorphisms, and VSD. Gene–environment interaction effects were analyzed through logistic regression models, with false discovery rate <i>p</i>-value (FDR_<i>p</i>) < 0.05. Maternal excessive intake of fermented bean curd (OR = 2.00, 95%CI: 1.59–2.52), corned foods (OR = 2.23, 1.76–2.84), fumatory foods (OR = 1.75, 1.37–2.23), grilled foods (OR = 1.34, 1.04–1.72), and fried foods (OR = 1.80, 1.42–2.27) was associated with an increased risk of VSD. Regular intake of fish and shrimp (OR = 0.42, 0.33–0.53), fresh eggs (OR = 0.58, 0.44–0.75), soy products (OR = 0.69, 0.56–0.85), and dairy products (OR = 0.71, 0.59–0.85) was found to reduce the occurrence of VSD. Moreover, <i>MTHFR</i> gene polymorphisms at rs2066470 (homozygous: OR = 4.28, 1.68–10.90), rs1801133 (homozygous: OR = 2.28, 1.39–3.74), and rs1801131 (heterozygous: OR = 1.75, 1.24–2.47; homozygous: OR = 3.45, 1.50–7.95) elevated offspring susceptibility to VSDs. Furthermore, significant interactions of <i>MTHFR</i> polymorphisms with maternal dietary habits were observed, encompassing corned foods, fermented bean curd, fried foods, and grilled foods. Maternal dietary habits; <i>MTHFR</i> polymorphisms at rs2066470, rs1801131, and rs1801133; and their interactions were significantly associated with the occurrence of VSDs in offspring.