Early childhood is the most important time for establishing healthy eating habits, and of course during this period a mother can have a great influence in this regard. In this study explored what major factors influence the development children’s food habits and whether the level of nutrition knowledge of parents has a material impact. This study involved 219 students (age renge, 3–5 years) and their parents in Osaka prefecture in Japan. Mothers were administered questionnaires that contained uestions pertaining to lifestyle, unidentifiable description of the children and their guardian’s SRH along with 39 questions to assess the food-related habits and attitudes. The correlates of the nutrition-related knowledge level of mothers and the children’s concern and respect for healthy eating were assessed using the Chi-square test, Fisher’s exact test and the Mann-Whitney U test. The differences between high and low amount of parental knowledge and high and low non-cognitive skills towards food groups were also examined. Completed questionnaires were returned by 219 of the participants. Among the respondents, 50.7% were male, and 92.2% of the parents indicated that they get nutrition information from the Internet. We remarkably found that the level of mother’s knowledge about nutrition had no statistically significant influence on how the children in this study understood food. However, chilren’s concern and respect for food were significantly associated with their participation in various aspects of food preparation (help with washing and cooking of food) and presentation (help with setting up the table) (P < 0.05, Mann–Whitney U test). Participation of Japanese kindergarten children in such activities was significantly associated with high level of food-related non-cognitive skills. Of note, the nutrition-related knowledge level of the mother showed no significant association with the attitude of their children towasds food.