The invention discloses a temperature uniformity control system for a multi-temperature zone of a large-plate vacuum annealing furnace and a control method thereof. The control system comprises a plurality of temperature controllers, a plurality of power regulators, a uniform temperature data logging device and an upper computer monitoring system, wherein the upper computer monitoring system is used for analyzing detection signals of the uniform temperature data logging device and monitoring the working process of each temperature controller and each power regulator. The control method comprises the following steps of: (1) initiating data; (2) working out the absolute value of the temperature difference e(n) and the absolute value of the temperature difference change rate ec(n); (3) setting control parameters required to be used by a PID (Proportion Integration Differentiation) controller on line by using a fuzzy reasoning method; (4) automatically setting the PID parameters; (5) controlling the heating of the vacuum annealing furnace; (6) detecting the temperature uniformity of the multi-temperature zone; and (7) analyzing and locally adjusting the temperature uniformity of the multi-temperature zone. The control system has the advantages of high temperature control accuracy, good temperature uniformity, high reliability and good adaptivity and robustness, the production process requirements of the rare metal vacuum annealing furnace can be well satisfied, and the control system is convenient for popularization and application.