Previous measurements (Del Rio et al. 2019) have confirmed the formation of cool summer microclimates through a combination of passive cooling elements (i.e., evaporative cooling louver, vegetation, and sunscreen) in semi-outdoor building spaces in Japan. Computational fluid dynamics (CFD) simulation is useful to understand the contribution of each element to semi-outdoor and indoor microclimates with natural ventilation, and to determine their effective combination. To date, there have not been sufficient studies on the modeling and validation for the CFD simulation of microclimates by such elements. This study demonstrates the modeling method using literature-based values and field measurements. It also demonstrates model validity by comparing the obtained results with field measurements. The results show that CFD simulation with detailed modeling of these elements can replicate vertical temperature distributions at four different positions across the semi-outdoor space and indoor space. The maximum difference in air temperature between the measurements and simulation results was 0.7–1 °C. The sensitivities of each passive cooling element on the microclimates formed in both spaces were confirmed. The watered louver condition and shorter louver–window distance were most effective in cooling both spaces. These results indicate that the modeling method could be effectively applied to assess cool microclimates and formulate a passive cooling design.