This study evaluated the association between maternal magnesium intake (MMI) and childhood wheezing incidence in 3-year-old offspring. We hypothesised that higher MMI imparts anti-inflammatory and antioxidant effects that decrease childhood wheezing incidence in offspring. Data of 79 907 women (singleton pregnancy, ≥ 22 weeks) from the Japan Environment and Children’s Study (enrolled between 2011 and 2014) were analysed. Participants were categorised into quintiles of MMI (< 148·00, 148·00–187·99, 188·00–228·99, 229·00–289·99 and ≥ 290·00 mg/d), quintiles of adjusted MMI for daily energy intake (aMMI) (< 0·107, 0·107–0·119, 0·120–0·132, 0·133–0·149 and ≥ 0·150 mg/kcal) and MMI levels either below or above the ideal value (< 310·00 or ≥ 310·00 mg/d). Multivariable logistic regression analysis was performed to calculate OR for the incidence of childhood wheezing in offspring among participants in each MMI category, with the lowest MMI group considered the reference group. Maternal demographic, socio-economic, medical and other nutrient intake backgrounds were considered potential confounding factors. The adjusted OR (aOR) for childhood wheezing in the offspring of women with the highest MMI was 1·09 (95 % CI, 1·00, 1·20), whereas that calculated based on aMMI categories and offspring of women with above-ideal MMI levels remained unchanged. The highest MMI was associated with slightly increased childhood wheezing incidence in the offspring. MMI during pregnancy had an insignificant clinical impact on this incidence; moreover, modifying MMI would not significantly improve childhood wheezing incidence in offspring. Therefore, further studies should clarify the association between other prenatal factors and childhood wheezing incidence in offspring.