In order to realize the "design by simulation" concept in the building design, the methodology of applying the building simulation in the building’s conceptual design stage is the main theme discussed in this paper. The conceptual design stage is divided into four sub-stages, and the framework of the design is built by way of the simulation in the conceptual design stage. Moreover, the energy saving potential assessment by the simulation in the preliminary conceptual design stage is also discussed in detail, including the input/output information, the calculation method and procedure, and the requirements and information from architects, etc. The natural ventilation design is used as the first trial in this study, and the difference between the detailed conceptual design and the preliminary conceptual design is also discussed, and the new simulation methodology is further described. The main objective of this paper is to help avoid an incorrect decision in the conceptual design stage, as well as to provide a better base for the energy efficient design in the next stage by means of the building simulation tool.