Maternal smoking during pregnancy is a risk factor for childhood obesity; however, the combined effect of secondhand smoking during pregnancy on children in the early years is unclear. We examined the effects of maternal active and secondhand smoking during pregnancy on childhood obesity in a large population-based cohort. A nested case–control study originating from the Japan Environment and Children’s Study was performed. The maternal smoking status was collected via self-administered questionnaires during mid/late pregnancy. Obesity in children was determined based on BMI measured at 3 years of age. In total, 4875 cases and 19,491 controls were included in the analyses. Conditional logistic regression models with a significance level of 5% (two-tailed test) were used to test the association. The proportion of mothers who continued smoking and who were exposed to secondhand smoking daily during pregnancy were 3.9% and 13.0% in cases and 2.9% and 10.8% in controls, respectively. Continuous maternal smoking was associated with increased odds of obesity compared to those who never smoked or quit smoking before the pregnancy (adjusted odds ratio, 1.39; 95% confidence interval, 1.01–1.92). The odds increased further when combined with secondhand smoking. The promotion of non-smoking among family members, in public and workplace could benefit pregnant women and offspring.