In order to increase the driving range of electric vehicle, while maintaining high thermal comfort inside the passenger cabin, it is necessary to design a control system which optimally synthesizes multiple control actions of heating, ventilation and air-conditioning (HVAC) system, while taking into account various constraints imposed by system hardware requirements. To this end, dynamic programming-based optimisation of HVAC control variables, which simultaneously minimises conflicting criteria of passenger thermal comfort and HVAC efficiency, is first proposed in the paper. Next, a hierarchical structure of thermal comfort control system is proposed, which consists of optimised low-level control loops, a superimposed cabin temperature controller that regulates cooling capacity, and optimisation-based control allocation strategy that sets references for inner HVAC control loop. Finally, the overall control system is verified by simulation for cool-down scenario, and the simulation results are compared with the DP benchmark.