The heating, ventilation and air conditioning (HVAC) system negatively affects the electric vehicle (EV) driving range, especially under cold ambient conditions. Modern HVAC systems based on the vapour-compression cycle can be rearranged to operate in the heat pump mode to improve the overall system efficiency compared to conventional electrical/resistive heaters. Since such an HVAC system is typically equipped with multiple actuators (compressor, pumps, fans, valves), with the majority of them being controlled in open loop, an optimisation-based control input allocation is necessary to achieve the highest efficiency. This paper presents a genetic algorithm optimisation-based HVAC control input allocation method, which utilises a multi-physical HVAC system model implemented in Dymola/Modelica. The considered control inputs include the cabin inlet air temperature reference, blower and radiator fan air mass flows and secondary coolant loop pumps’ speeds. The optimal allocation is subject to specified, target cabin air temperatures and heating power. Additional constraints include actuator hardware limits and safety functions, such as maintaining the superheat temperature at its reference level. The optimisation objective is to maximise the system efficiency defined by the coefficient of performance (COP). The optimised allocation maps are fitted by proper mathematical functions to facilitate the control strategy implementation and calibration. The overall control strategy consists of superimposed cabin air temperature controller that commands heating power, control input allocation functions, and low-level controllers that ensure cabin inlet air and superheat temperature regulation. The control system performance is verified through Dymola simulations for the heat pump mode in a heat-up scenario. Control input allocation map optimisation results are presented for air-conditioning (A/C) mode, as well.