Background The prevalence of flexible flatfoot is high among preschool-aged children, but the effects of treatment are inconclusive due to the unclear definitions of normal flatfoot. To date, a universally accepted evaluation method of the foot arch in children has not been completely established. Our aims of this study were to establish a new method to evaluate the foot arch from a three dimensional perspective and to investigate the flexibility of the foot arch among children aged from two to six. Methods A total of 44 children aged from two to six years of age were put into five age groups in this study. The navicular height was measured with one leg standing, and both feet were scanned separately in both sitting and one leg standing positions to compute the foot arch volume. The arch volume index, which represents the ratio of the difference in volume between sitting and one leg standing positions to the volume when sitting was calculated to demonstrate the flexibility of the foot arch. The differences of measured parameters between each aged group were analyzed by one-way ANOVA. Results The arch volumes when sitting and standing were highly correlated with the navicular height. The navicular height ranged from 15.75 to 27 mm, the arch volume when sitting ranged from 6,223 to 11,630 mm3, and the arch volume when standing from 3,111 to 7,848 mm3 from two to six years of age. The arch volume index showed a declining trend as age increased. Conclusion This study is the first to describe the foot arch with volume perspective in preschool-aged children. The foot arch volume was highly correlated with the navicular height. Research results show both navicular height index and arch volume index gradually increase with age from two to six. At the same time the arch also becomes rigid with age from two to six. These results could be applied for clinical evaluation of the foot arch and post-treatment evaluation.