Increasing the energy efficiency of existing buildings is the major strategy to reach carbon neutral targets, given that the building sector is a major emitter. In particular, one major part of building energy usage is the building heating, ventilation and air-cooling system, which are highly depending on the thermal performance of building envelope and increase the challenge of selecting optimal packages of energy efficiency measures. This paper thereby presents a method for optimizing the building envelope and heating, ventilation and air-cooling system. The simulation-based NSGA-III approach developed in this paper is based on coupling the dynamic simulation models created in EnergyPlus software with the non-dominated sorting genetic algorithm, as the engine that performs an optimization process. A large domain of energy efficiency packages combined with heating, ventilation and air-cooling systems and building envelope are investigated to minimize energy consumption, retrofit cost and thermal discomfort in indoor environments, which including ideal loads air system, four pipe fan coil system and variable refrigerant flow system, insulation materials and insulation thickness for external walls and roof, different types of external windows, and window-wall ratio. An office building in Chongqing was chosen as a case study to demonstrate the practical implementation of the proposed method. The results show that the four pipe fan coil system was superior in the diversity and performance of the Pareto front. Then, the optimal packages were generated by a synthetic method, which have 58.57 kWh/m2 of energy consumption, 30.76 CNY/m2 of retrofit cost and 40.67 % of the percentage of thermal discomfort hours. The results also indicate that the yearly energy savings rates are 17.30 %, 23.05 % and 21.10 % separately for ideal loads air system, four pipe fan coil system and variable refrigerant flow system after performing optimization. These results highlight the importance and necessity of performing an optimization procedure for existing buildings to select the optimal retrofit measures.