Evidence links exposure to maternal sulfur dioxide (SO2) and the risk of limb defects have been inconsistent. To investigate associations between SO2 exposure during preconception and the first trimester and risks of polydactyly and syndactyly. The study population was acquired from the Maternal and Child Health Certificate Registry of Liaoning Province between 2010 to 2015, and consisted of 2605 polydactyly, 595 syndactyly cases, and 7950 controls. Ambient air pollutants levels were retrieved from air quality monitoring stations. We used multivariable logistic regression model to assess the adjusted odds ratios (ORs) and 95% confidence intervals (CIs). We found that exposure to increased SO2 concentrations was associated with polydactyly during both the 3 months preconception (ORQ4 vs. Q1 = 3.76; 95% CI 2.61, 5.42; per 10 μg/m3 increment: OR = 1.07; 95% CI 1.04, 1.10) and the first trimester (ORQ4 vs. Q1 = 2.03; 95% CI 1.41, 2.92; per 10 μg/m3 increment: OR = 1.07; 95% CI 1.03, 1.11). However, we only observed increased risk for syndactyly in the analysis of high vs. low quartiles (three months preconception: ORQ4 vs. Q1 = 3.72; 95% CI 2.05, 6.75; first trimester: ORQ4 vs. Q1 = 1.98; 95% CI 1.11, 3.51). Most results of analyses based on single-month exposure window generally showed similar positive associations. Additionally, these findings were broadly consistent across subgroups and sensitivity analyses. Maternal SO2 exposure increase the risk of polydactyly and syndactyly.