Rural dwellings are an important group of residential buildings in China. With the continuous development of rural construction in China, the contradiction between the pursuit of a simple material space and the villagers’ demand for living quality, especially the indoor thermal comfort of rural dwellings, has become increasingly prominent. Therefore, it is particularly important to study the optimization strategies of the indoor thermal environment in rural dwellings. Current research on optimizing the indoor thermal environment of rural dwellings mainly focuses on analyzing the impact of individual factors, such as the envelope structures, building constructions, and building technology applications, but there is a lack of strategy development based on the comprehensive evaluation. This study aims to analyze the combined effects of multiple design elements on the indoor thermal environment and propose a comprehensive optimization strategy for rural dwellings. This study selects the rural dwellings around Xi’an as an example and establishes a basic model of the rural dwellings around Xi’an through field investigation and software simulation. Then, through univariate and compound-variable simulations, we analyze the influence of changes in passive architectural design indicators on the indoor physiological equivalent temperature (PET) of rural dwellings and obtain a comprehensive design indicator optimization strategy. This strategy can improve the indoor thermal comfort in winter and summer, especially in winter, achieving an average increase of 4.17 °C in the winter PET value and an average decrease of 0.66 °C in summer. This provides a reference for the design and renovation of rural dwellings in Xi’an and other rural areas in the cold regions of China.