This study examined the relationships between the foot bone morphologies and sprint performance in sprinters. Foot images in 56 male sprinters obtained using magnetic resonance imaging. The relative lengths of the forefoot bones of the big and second toes, which were calculated as total lengths of the forefoot bones for each toe normalized to the foot length, correlated significantly with personal best 100-m sprint time (r = − 0.293 and − 0.459, both Ps < 0.05). The relative lengths of the rearfoot talus and calcaneus normalized to the foot length also correlated significantly with the sprint performance (r = − 0.378 and − 0.496, both Ps < 0.05). Furthermore, the relative height of the calcaneus, but not the talus, normalized to body height correlated significantly with sprint performance (r = − 0.690, P < 0.001). Additionally, the relative calcaneus height correlated significantly with the foot arch height index (r = 0.420, P = 0.001), and the foot arch height index correlated significantly with sprint performance (r = − 0.517, P < 0.001). These findings suggest that the taller calcaneus may be a key morphological factor for achieving superior sprint performance, potentially via modeling the longer forefoot and rearfoot bones and functional foot morphology in sprinters.