Providing thermal comfort in the courtyards of academic buildings is important and increasing tree canopy coverage (TCC) presents a convenient and feasible method to achieve this; however, few studies have comprehensively evaluated the cooling effects of TCC, considering both outdoor thermal comfort and heat dynamics. In this study, we selected two typical academic buildings at Guangzhou University, each with courtyards having different height-to-width ratios (H/W ratios). We employed both field measurements and ENVI-met-based numerical models to simulate scenarios with varying TCCs. The results demonstrated that the cooling effects caused by arranging trees increase with the TCC values. During the hottest hours of the day, trees arranged in courtyards with high H/W ratios exhibited a superior cooling effect compared to those in courtyards with low H/W ratios, with a difference of up to 0.6 °C in the PET (physiological equivalent temperature); however, over the entire daytime, the total sensible heat reduction achieved by trees in courtyards with low H/W ratios surpassed that of courtyards with high H/W ratios, with a difference of up to 0.25 × 104 J/m2. Our findings underscore the crucial role of TCC in enhancing cooling in the courtyard of academic buildings, with important implications for university planning and design.