Running is beneficial for physical health, but it is also accompanied by many injuries. However, the main factors leading to running injury remain unexplained. This study investigated the effects of long running distance on lower-limb kinematic variables and the lower limb kinematic difference of between the initial (IR) and terminal phase (TR) of 5 km running was compared. Ten amateur runners ran on a treadmill at the speed of 10 km/h. Dynamic kinematic data was collected at the phase of IR (0.5 km) and TR (5 km), respectively. The peak angle, peak angular velocities, and range of motion were recorded in this experiment. The main results demonstrated the following: ankle eversion and knee abduction were increased at TR; ROMs of ankle and knee were increased in the frontal plane at TR than IR; a larger peak angular velocity of ankle dorsiflexion and hip interrotation were found in TR compared to IR. These changes during the long distance running may provide some specific details for exploring potential reasons of running injuries.