The invention relates to a flue gas heavy metal concentration measurement technology, and discloses a flue gas heavy metal monitoring system and a monitoring method thereof. The flue gas heavy metal monitoring system comprises a sampling device, an absorption device, a detection device, a first liquid storage tank, a second liquid storage tank and a display control device, wherein the sampling device comprises a sampling pipeline, a filtering unit, a pressure regulating unit and a sampling power unit, the two ends of the sampling pipeline are connected with a flue, the filtering unit is located in the sampling pipeline and close to the inlet end of the sampling pipeline, the pressure regulating unit is located on the sampling pipeline and close to the outlet end of the sampling pipeline, the absorption gas inlet end of the absorption device is connected with the area, where the filtering unit is located, of the sampling pipeline, the first liquid storage tank and the second liquid storage tank are connected with the absorption device through a pumping unit, the second liquid storage tank is connected with the detection device, and the sampling power unit, the pumping unit and the detection device are electrically connected with the display control device. According to the monitoring system, the concentration of various gaseous heavy metals in the flue gas can be automatically monitored on line, and the detection precision is high.