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The purpose of this study was to explore if the tri-axial linear acceleration and angular velocity of knee and ankle joints differ between barefoot and minimal footwear running through investigating the extreme value difference. Eight participants were recruited for this experiment, acceleration parameters were measured utilizing IMU sensors. For the angular velocity, the minimum value in the frontal plane (p = 0.028) showed a decrease in the ankle joint. The minimal value in the sagittal plane and maximal value in the transverse plane (p = 0.001, p = 0) increased significantly. For the knee joint, the extreme values in the frontal plane increased (p = 0, p = 0), the maximal value increased and minimal value decreased with p = 0 and p = 0 in the sagittal plane. A significant decrease in the maximal value (p = 0) was exhibited in the transverse plane. The increased angular velocity may contribute to a result, with an insufficient arch support condition (minimalist shoes running) causing the foot’s intrinsic and extrinsic muscles and lower limb joints injury. These injuries should be a consideration for the novice minimalist runners.