The purpose of the present study was to clarify comprehensively how and to what extent inhibition, spatial working memory (WM), and auditory WM influence agility, balance, and dexterity of motor coordination and comprehensive physical ability in kindergarteners. Participants were 43 children between the ages of 4 and 5 years old. The children performed executive function (inhibition and WM) and motor coordination tasks, and a teacher evaluated their comprehensive physical abilities. Results showed that spatial WM was significantly related to auditory WM, executive functions were significantly related to agility, and agility was significantly related to comprehensive physical ability. Furthermore, using structural equation modelling, we investigated whether executive functions influenced comprehensive physical ability via motor coordination. Results showed a significant correlation between spatial WM and auditory WM. Executive functions, including inhibition, spatial WM, and auditory WM, predicted comprehensive physical ability via agility of motor coordination in the kindergarteners.