With the rise of energy-saving’s importance in building design, passive house design has become popular method as a means of improving heating/cooling performance of buildings. A lot of countries are promoting the construction and distribution of low-energy buildings since the largest savings in energy-use can be obtained in new buildings through building design and operating plan. Among numerous elements of passive house design process, energy simulation is very important since it heavily affects the form, use of building material, and cost. This paper proposes coupling of conventional multi-zone method and CFD to calibrate the energy simulation results. The coupling of two simulation methods enables analysis of microclimate modifications in building design. The proposed method combines advantages of EnergyPlus and CFD, using a multi-scale approach that analyzes the flows using the multi-scales between macro- and microclimates. 1-year performance of a single-family house located in Korea was conducted by using a single EP and a passive house design combined with microclimate design method. The result shows that microclimate method can reduce more thermal variances. Thermal variances in simple passive method are larger than 10 ℃ but the combination with microclimate has smaller variances of 5℃ to 10℃. The reduced thermal variances in the energy simulation provide accurate energy data. Therefore, it will help designers to make better decisions for building structure, materials for optimized energy-saving building design. Moreover, use of microclimate design elements from the early design stage also improve the airflow between outdoor and indoor in summer and enable to utilize inter-zone air current in winter. Consequently, higher indoor temperatures in winter and lower temperatures in summer are obtained.