Tourism has become one of the most prosperous economic activities, especially in rural areas; but, due to destinations’ dependence on this industry and the increasing ease of travel for tourists, many tourism destinations have faced challenges such as overtourism. Overtourism is recognized as the negative impact of excessive visitor congestion, which on the one hand can reduce the quality of life for host communities and on the other hand disrupt the delivery of memorable experiences to tourists. Therefore, ensuring the resilience of destinations against shocks—including overtourism—is essential. For this reason, governments and policymakers, due to their access to extensive resources, are considered the best option for enhancing the resilience of these destinations. Accordingly, the present study aimed to identify governance structure strategies to enhance the resilience of rural destinations in Torghabeh–Shandiz County in the face of overtourism. The research method was a combination of descriptive–analytical approaches and mixed quantitative–qualitative methods. Data collection was conducted through both library research—using documents and records—and fieldwork using interviews and questionnaires. The study sample included local and supra-local managers within the tourism organizational structure as well as researchers in this field, selected through snowball sampling. Then, to analyze and determine the importance of the 18 extracted strategies, the Importance–Performance Analysis (IPA) method was applied. Overall, the results indicate that implementing smart traffic limitations, especially during holidays and peak seasons, holds the highest importance in addressing overtourism.