Our previous study suggested that children’s food preferences were related to their concern about food and respect for food. In general, concern and respect were sorts of non-cognitive skills, which are useful for future life if acquired during childhood. The aim of this study was to make clear how concern about food and respect for food were related to their food habits and life style. We investigated the relationship between children’s non-cognitive skills and their food habits in a cross-sectional study. From 2007 to 2016, 2,408 Japanese kindergarten children aged 3 to 5 years were included in the study. The distribution was categorized into two patterns of their non-cognitive skills based on whether a particular the guardians answered children’s non-cognitive skills, concern about food and respect for food. The high and low of non-cognitive skills toward food were related to lifestyle, food preferences and food habits. High non-cognitive skills toward food may be associated with to take good food habits and their preferences in kindergarten children.