This study aims to examine relations between Chinese preschoolers’ physical well-being (physical fitness and motor skills), executive functioning, and academic skills (receptive language, math, and science skills) at the end of the Kindergarten year, the last year of preschool in the Chinese early childhood education system. A total of 273 children (141 boys and 132 girls) from 30 preschools stratified by urbanicity were examined on physical fitness and motor skills at ages 4 to 5 years, and later on receptive language, math, and science performance one year later before they exited the Kindergarten year. Findings first revealed a direct effect of physical fitness on academic skills at the between-school level. Next the between-school indirect effect of physical fitness on academic skills and the within-school effect of motor skills on academic skills, via executive functions, were found to be significant. Specifically, schools with better physical fitness had higher mean levels of executive function which in turn related to higher mean levels of academic skills (the between variance reduction was 19.3%), and children with better motor skills had greater executive functions and then gained more academic skills within a school (the within variance reduction was 4.1%). This study underscores the importance of physical well-being on children's outcomes at a critical transition point of schooling. Discussion on findings, the implications for practice and policy as well as the limitations of this study were followed.