Achieving comfort in hot summer and cold winter (HSCW) climate zones can be challenging, since the climate is characterized by high temperatures in the summer and relatively colder temperatures in the winter. Courtyards, along with other semi-open spaces such as verandas and overhangs, play an important role in mitigating outdoor climate fluctuations. In this research, the effects of courtyards on the thermal performance of vernacular houses in HSCW climate zones were studied via field measurements and computational fluid dynamics (CFD) models. The selected courtyard house was a representative vernacular timber dwelling situated in the southeast of Chongqing, China. The indoor and outdoor air temperature measurements revealed that the courtyard did play an active role as a climatic buffer and significantly reduced the temperature’s peak value in the summer, while during the winter, the courtyard prevented the surrounding rooms from receiving direct solar radiation, and thus to some extent acted as a heat barrier. The contributions of thermal mass are quite limited in this area, due to insufficient solar radiation in winter and general building operations. The natural ventilation mechanism of courtyard houses in HSCW zones was further studied through CFD simulations. The selected opened courtyard was compared to an enclosed structure with similar building configurations. The airflow patterns driven by wind and buoyancy effects were first simulated separately, and then together, to illustrate the ventilation mechanisms. The simulation results show that the courtyard’s natural ventilation behavior benefited from the proper openings on ground level.