Foot morphology and function has received increasing attention from both biomechanics researchers and footwear manufacturers. In this study, 168 habitually unshod runners (90 males whose age, weight & height were 23±2.4 years, 66±7.1 kg & 1.68±0.13 m and 78 females whose age, weight & height were 22±1.8 years, 55±4.7 kg & 1.6±0.11 m) (Indians) and 196 shod runners (130 males whose age, weight & height were 24±2.6 years, 66±8.2 kg & 1.72±0.18 m and 66 females whose age, weight & height were 23±1.5 years, 54±5.6 kg & 1.62±0.15 m) (Chinese) participated in a foot scanning test using the easy-foot-scan (a three-dimensional foot scanning system) to obtain 3D foot surface data and 2D footprint imaging. Foot length, foot width, hallux angle and minimal distance from hallux to second toe were calculated to analyze foot morphological differences. This study found that significant differences exist between groups (shod Chinese and unshod Indians) for foot length (female p = 0.001), width (female p = 0.001), hallux angle (male and female p = 0.001) and the minimal distance (male and female p = 0.001) from hallux to second toe. This study suggests that significant differences in morphology between different ethnicities could be considered for future investigation of locomotion biomechanics characteristics between ethnicities and inform last shape and design so as to reduce injury risks and poor performance from mal-fit shoes.