Buildings contribute to a major part of energy consumption in urban areas, especially in areas like Hong Kong which is full of high-rise buildings. Smart buildings with high efficiency can reduce the energy consumption largely and help achieve green cities or smart cities. Design and control optimization of building energy systems therefore plays a significant role to obtain the optimal performance. This paper introduces a general methodology for the design and control optimization of building energy systems in the life cycle. When the design scheme of building energy systems is optimized, primary steps and related issues are introduced. To improve the operation performance, the optimal control strategies that can be used by different systems are presented and key issues are discussed. To demonstrate the effect of the methods, the energy system of a high-rise building is introduced. The design on the chilled water pump system and cooling towers is improved. The control strategies for chillers, pumps and fresh air systems are optimized. The energy saving and cost from the design and control optimization methods are analyzed. The presented methodology will provide users and stakeholders an effective approach to improve the energy efficiency of building energy systems and promote the development of smart buildings and smart cities.