The campus courtyards in the Lingnan area are commonly used spaces. Therefore, their thermal comfort is highly important for improving user satisfaction. This study conducted field research on 18 courtyards in four universities in Lingnan to explore the effects of their architectural design factors on the thermal environment. Relevant studies have proved that courtyards are cost-effective in microclimate regulation, and individual factors such as the scale and openness of the courtyards have also been shown to have an effect on the thermal comfort of the courtyards. This study synthesizes multidimensional architectural design factors to explore and analyze the thermal environments of college courtyards. Physiologically equivalent temperature (PET) is selected as the thermal comfort evaluation index for the study and the conclusions are as follows: (1) The thermal environment is the most important factor influencing visitors to the courtyards (22%), and good thermal comfort improves the efficiency of using the college courtyards; (2) the courtyards have a positive microclimate regulating function, and a cooling effect occurs in 80% of them; and (3) the floor location, type, orientation, and sky view factor (SVF) of the courtyards are the main design factors affecting the thermal environment and PET. The first three factors were negatively correlated with PET (p < 0.05),and SVF was positively correlated with PET (p = 0.651). Passive courtyard design strategies are presented based on the findings of this study.