The rising energy demand for buildings has enhanced public awareness of sustainable energy sources and technologies. In particular, natural ventilation systems such as wind-catchers have attracted considerable new attention. A new wind-catcher design with single-stage direct-air evaporative cooling was proposed for indoor air conditioning. An Eulerian-Lagrangian approach employing the Realizable k-ε model was utilized to conduct the CFD simulations. Furthermore, the effects of inclining the bottom surface of the wind-catcher and installing a baffle across the flow path on the air temperature drop, water mass fraction, and air velocity distribution were studied. The inclined bottom surface led to more flow uniformity in the room compared to the conventional geometry. The baffled wind-catcher with β = 0, 30, 45, and 60° and unbaffled wind-catcher showed different flow patterns and thermal comforts. A methodology for evaluating the thermal comfort performance of evaporative cooling systems integrated into natural or passive cooling devices was also proposed based on the generated CFD results. The baffled wind-catcher with β = 60° combined with an evaporative cooling system significantly reduced the air temperature inside the building up to 17.4 °C and improved the occupants’ thermal comfort. The most suitable design for thermal comfort was also determined.