The purpose of this study is to investigate the differences of the first metatarsophalangeal joint’s 6 degree-of-freedom (6DOF) kinematics during shod and barefoot conditions by using a high-speed dual fluoroscopic imaging system (DFIS). Fifteen healthy male runners were recruited. Computed tomography (CT) scans were taken of each participant’s right foot for the construction of 3D models and local coordinate system. The fluoroscopic images of the right foot during the stance period were acquired under shod and barefoot condition with rearfoot strike pattern Radiographic images were acquired at 100 Hz while the participants ran at a speed of 3±5% m/s in a track and 6DOF kinematics were calculated by 2D-3D registration. Paired sample t-test was used to compare the kinematic characteristics of the first MTPJ 6DOF kinematics between shod and barefoot. Compared with barefoot, wearing shoes 1) decreased the peak medial, posterior, and superior translation of the first MTPJ during stance (P < 0.05); 2) decreased maximum extension angle, minimum extension angle, and flexion/extension range of motion of the first MTPJ during stance (P < 0.05); 3) increased minimum adduction angle of the first MTPJ during stance (P < 0.05). It suggests that shoes may affect the function of the first MTPJ and increase the risk of hallux valgus. Our study makes up for the deficiency of traditional motion measurement methods that only focus on the sagittal flexion and extension movement of the first MTPJ and provides a more comprehensive understanding of the potential relationship between joint motion and injurie