The number of houses with large, continuous spaces has increased recently. With improvements in insulation performance, it has become possible to efficiently air condition such spaces using a single air conditioner. However, the air conditioning efficiency depends on the placement of the air conditioner. The only way to determine the optimal placement of such air conditioners is to conduct an experiment or use computational fluid dynamic analysis. However, because the analysis is performed over a limited period, it is difficult to consider non-stationarity effects without using an energy simulation. Therefore, in this study, energy simulations and computational fluid dynamics analyses were coupled to develop a thermal environment analysis method that considers non-stationarity effects, and various air conditioner arrangements were investigated to demonstrate the applicability of the proposed method. The accuracy verification results generally followed the experimental results. A case study was conducted using the calculated boundary conditions, and the results showed that the placement of two air conditioners in the target experimental house could provide sufficient air conditioning during both winter and summer. Our results suggest that this method can be used to conduct preliminary studies if the necessary data are available during design or if an experimental house is used.