A vehicle body tracking system of a vehicle assembly line determines, in real time, a position of a vehicle body transferred to process sections divided by a predetermined pitch. The tracking system includes: a vehicle body detecting unit installed at a starting point of the assembly line so as to detect the vehicle body; an encoder unit provided at a conveyor unit, which travels along the assembly line and transfers the vehicle body, so as to detect a rotation amount of a rotating body rotated by a traveling body of the conveyor unit; and a controller to receive a detection signal from the vehicle body detecting unit to acquire identification information of the vehicle body and to calculate a moving distance of the vehicle body for each process section by receiving the detection value from the encoder unit.