<p>Archaeological sites are subject to various threats depending on their microenvironments, and existing research often fails to address the comprehensive management of these factors and their practical implementation. This study examines the Jinsha Earthen Site to explore the influence of external climatic conditions on the indoor environment. By analyzing factors such as light, temperature, and relative humidity, the study investigates temperature and humidity variations across different site areas and seasons. It also considers the effects of building structures, groundwater level fluctuations, and illumination intensity on the microenvironment. One-way analysis of variance (ANOVA) is employed to identify key control variables. A quantitative assessment method based on salt phase changes and risk zones is proposed, utilizing the VTT model to evaluate mold growth and assessing the microenvironment from the perspective of visitor comfort. Based on these analyses, the study offers systematic environmental control recommendations aimed at balancing site preservation standards with practical feasibility. The results indicate that indoor temperature and humidity are significantly influenced by external conditions, as well as by light and groundwater levels. Groundwater control measures reduced the occurrence of high-risk salt formations from 99% to 76% but also led to an 18% increase in phase changes, while reducing the mold growth index in damp areas by 81%. The microenvironment in various zones and periods did not meet visitor comfort standards, with high humidity and low temperatures identified as primary issues. This paper proposes comprehensive environmental control recommendations, including optimizing the management pathway, and implementing stratified, zoned, and time-segmented microenvironment management strategies. The research findings not only enhance the protective environment of the Jinsha Earthen Site but also provide valuable insights for similar indoor archaeological sites.</p>