Skywells are crucial for climate regulation in traditional Chinese dwelling architecture, exhibiting significant variations across climatic regions. This study focuses on humid–hot China, using Huangshan, to explore skywell parameters’ impact on thermal comfort and energy efficiency. Field research on 24 buildings in the World Heritage Site Xidi, Hong Villages, and Chinese Historical Pingshan Village, combined with Grasshopper’s Ladybug tool, established a parametric model. Using orthogonal design, performance simulation, and Python-based machine learning, six morphological parameters were analyzed: width-to-length ratio, height-to-width ratio, orientation, hall depth, wing width, and shading width. After NSGA-II multi-objective optimization, the summer Percentage of Time Comfortable (P_TC) increased by 5.3%, 38.14 h; the Universal Thermal Climate Index (UTCI) relatively improved by 2%; energy consumption decreased by 8.6%, 0.14 kWh/m²; and the useful daylight illuminance increased by 28%, 128.4 h. This confirms the climate adaptability of courtyard-style buildings in humid–hot China and identifies optimized skywell parameters within the study scope.