The invention relates to a chaotic composite stirring system and a stirring method thereof, and belongs to the technical field of mechanical stirring equipment. The chaotic composite stirring system comprises a chaotic composite stirring device and a monitoring control system, wherein the chaotic composite stirring device comprises a stirring tank, a stirring component, a driving device, a transmission device, a top-blown rotational flow spray gun, a side-blown rotational flow spray gun, a bottom-blown rotational flow spray gun, an air inlet pipe I, an air inlet pipe II and an air inlet pipe III; the monitoring control system comprises a high-speed camera, a laser transmitter, a processor and an electrical conductivity meter. According to the chaotic composite stirring system disclosed bythe invention, combination of mechanical stirring and rotational flow gas stirring in variable-frequency flow is adopted, the area of a chaotic mixing zone can be strengthened by freely changing an eccentricity ratio of the stirring tank, the immersion depth of a stirring shaft and a deviation angle, the gas spray quantities of rotational flow spray guns can be subjected to variable-frequency regulation in real time and can be in periodic pulsation change, the chaotic composite stirring device is enabled to realize chaotic mixing within an extremely short time under low Reynolds number flow, and the mixing efficiency and the heat and mass transfer speed of fluid materials are improved to a large extent.