Background To prevent increasing childhood obesity and non-communicable diseases (NCDs) among women in sub-Saharan Africa, as well as to understand the factors of food consumption in the population, this study aimed to identify the relationship between overweight/obesity and dietary intake among children and mothers in urban and rural Malawi.Methods We conducted anthropometric measurements (height, weight and MUAC) for children and mothers, blood pressure measurements for mothers, questionnaire interview with mothers with children aged 2-4.9 years in Lilongwe City (an urban area) and Mzimba District North (a rural area). Dietary survey was consisted of the 24-hour recall method and food frequency questionnaires (FFQ). Participants' mothers were classified as overweight/obese (BMI ≥ 25) and normal weight (18.5 ≦ BMI < 25). Nutrients, food consumption, FFQ, MDDW, MDD, and questions at p < 0.05 in the χ2 test and t-test for independent samples were performed a logistic regression analysis.Results Of 229 pairs, 200 pairs mother and children were analyzed in this study. Consequently, 37.5% (urban 34.0% and rural 40.2%) of mothers were classified as obese (BMI ≥ 25), and 4.5% (urban 8.0% and rural 1.8%) of children were classified as overweight (WHZ ≥ 3). According to our logistic regression analyses, fats and egg intake were positively associated with obesity in urban mothers, while carbohydrates (nsima) intake, number of deliveries, family history of NCDs, and increased income were positively associated with obesity in rural mothers. On the other hand, meat and fish intake were negatively associated with obesity in urban mothers, while rice, fats, and egg intake, and children’s diverse food intake (MDD-IYCF ≥ 5) were negatively associated with obesity in rural mothers.Conclusions The dietary factors related to the mother’s obesity differed in urban and rural areas. In rural area, the dietary diversity of children was a determinant to prevent obesity among mothers. To prevent childhood obesity and NCDs in Malawi, they are necessary to through the life course appropriate approach considering the areas and targets, and child nutrition education for mothers may prevent mothers' NCDs as well as child growth and health.