The Huizhou folk dwelling houses are important carriers of the traditional Huizhou cultural and architectural heritage in China. However, such dwelling houses have obvious shortcomings such as damp, dark, insufficient lighting, and inability to cope with cold weather. Existing studies on Huizhou folk dwelling houses haven’t considered factors such high humidity or low temperature that can lead to poor indoor thermal environment in winter, and few have concerned about the theoretical analysis on the formation mechanism of the indoor thermal environment. Therefore, to fill in this research blank, this paper aims to give thermal environment analysis and thermal comfort evaluation on the Huizhou folk dwelling houses under the guidance of auxiliary interior space layout. At first, this paper took the first courtyard of the typical “series-courtyard” structure of the Huizhou folk dwelling houses as the subject, and analyzed the thermal environment of the second courtyard, including the outer wall, door, roof, patio, and ground, and the amount of heat transfer, the amount of radiant heat, and the amount of heat exchange of ventilation were tested. Then, based on the location selection, layout, and architectural morphology of the Huizhou folk dwelling houses, this paper studied the relationship between the thermal comfort of Huizhou folk dwelling houses and the wind and heat environment in winter, the specific test items were indoor temperature, comfort degree, wall temperature, and air tightness, and the test results could provide basis and direction for the renovation of indoor thermal environment of Huizhou folk dwelling houses. At last, this paper gave the analysis results of an actual example, and verified the effectiveness of the analysis and evaluation methods in this paper.