In this paper, a cluster sampling method was used to randomly select 1308 young children from the southern part of Fujian Province, China, and the short format of the International Physical Activity Questionnaire (IPAQ) was used to investigate their physical activity. Logistic regression was used to analyze the influencing factors of children’s moderate-to-vigorous physical activity (MVPA) time. Results: The MVPA time deficit rate of urban migrant children in southern Fujian was 90.1%, and that of girls (92.2%) was significantly higher than that of boys (88.5%); Multivariate logistic regression analysis found that gender, parents’ support on sports, and sports grounds near their homes were the main factors affecting the lack of MVPA time for urban migrant children.