The invention discloses a lead-bismuth stacking and reloading machine control system and a method thereof. The control system comprises a programmable logic controller, multiple pieces of sub-equipment and multiple drive motors corresponding to the sub-equipment. The sub-equipment and the drive motors are provided with absolute value encoders. The absolute value encoders are used for measuring state information of the corresponding sub-equipment and the corresponding drive motors in real time respectively. The programmable logic controller is used for receiving the state information and controlling the corresponding drive motors to drive the corresponding sub-equipment to execute corresponding sections according to the state information, fed back by the absolute value encoders in real time, of the corresponding sub-equipment and the corresponding drive motors. By means of the lead-bismuth stacking and reloading machine control system and the method thereof, the efficiency and the safety of lead-bismuth pile in-pile reloading system can be improved, and the requirements of the functions, the process and safe reloading of a lead-bismuth pile are better met.