Rural dwellings are often self-designed and self-built by their owners, with construction decisions based on experience and imitation of nearby buildings. As existing advanced design methods are often too complex or resource-intensive for rural contexts, balancing cost-efficiency, energy performance, and functional needs remains a challenge. This paper proposes to use the matrix analysis method, which is a relatively simple and easy-to-learn procedure, to identify the optimal design of rural houses. Taking Hebi, located in the Central Plains of China, as an example, field research was carried out, and a baseline model was established. A number of variable models were analysed using the control variable method for building orientation and indoor headroom, and metrics such as energy consumption, uncomfortable hours and construction costs were calculated to screen out effective metrics. Furthermore, by combining matrix analysis with orthogonal tests, the approach enables the development of optimal design solutions more efficiently and with reduced complexity. The results show that the optimised design, generated using the proposed method, significantly improves the indoor thermal environment—reducing energy consumption by 65.26% and uncomfortable hours by 29.22%, with only a 1.3% increase in construction costs. This study contributes to sustainable rural development by proposing a practical framework that guides the design of low-cost and energy-efficient rural housing.