The invention provides a central air-conditioning control system and a control method thereof, and belongs to the technical field of air-conditioning systems. The central air-conditioning control system comprises a universal equipment model library, an equipment performance testing module, a comfort level evaluating module, a genetic algorithm multi-objective optimization control module and an execution module. An actual measured method is used, a system model is established, and the central air-conditioning control system is high in precision and high in reliability and is adaptive; a genetic algorithm is used, multi-objective optimizing can be realized, the optimizing efficiency is high, the comfort level is high, energy is saved, and the cost is low; whether a user feels comfortable or not can be intelligently judged by a user behavior recognition mode, and control objectives are adjusted in time; and the control method can be optimal on the basis of environmental change, particularly at the transition season, the equipment efficiency can be greatly improved, and energy conservation and emission reduction are realized.