The traditional Yikeyin dwellings in central Yunnan exhibit a distinctive spatial layout and skywell design that passively adapt to the mild plateau monsoon climate through natural ventilation. Although their courtyard-based configuration and skylight design are widely recognized for climatic adaptability, the quantitative relationship between courtyard orientation and ventilation performance remains insufficiently explored. This study integrates on-site environmental monitoring with validated Computational Fluid Dynamics (CFD) simulations to investigate how different courtyard orientations influence airflow organization and the indoor thermal environment. Based on detailed field surveys and measured data, three representative orientation schemes were established. The RNG k-ε turbulence model was adopted, and one-way coupled simulations using OpenFOAM and EnergyPlus were conducted to evaluate seasonal ventilation behavior and indoor thermal comfort. The findings reveal synergistic design principles between building orientation and courtyard spatial configuration, as well as spatial differentiation patterns contributing to thermal environment stability. Three orientation types—leeward, windward, and transitional—were identified, each demonstrating distinct advantages and limitations. The study quantitatively confirms the effectiveness of Yikeyin dwellings in utilizing natural ventilation for environmental regulation during both summer and winter seasons. These results provide scientific evidence and design support for modern buildings seeking to achieve enhanced ventilation performance and climatic adaptability.