Historical sites are incomplete relics left by human activities and are also valuable resources for human society, with most of them buried deep underground. Because the protection of original historical sites is difficult, very few sites choose this method. Many funerary objects that have been in historical sites are scattered in museums, losing their original context and complicating their utilization. Thus, using digital technology to protect and utilize historical sites and to explore their outstanding value from historical, aesthetic, and anthropological perspectives is a foremost concern. Therefore, this study aims to develop a comprehensive method for the protection and utilization of historical sites, that is, digital protection and utilization based on a digital twin. We constructed a historical site digital twin model using qualitative and vertical methods, including a physical entity, virtual entity, twin data center, digital twin service, and connection. We also established a technical framework of data acquisition and processing, digital protection, and digital utilization, forming a layered management and application of digital resources. In digital protection, information in the real world and the virtual world are connected to monitor risks, collect data, create simulations, and propose protection strategies, quickly and accurately. In digital utilization, the knowledge graph is constructed to associate seemingly unrelated information, explore potential knowledge, and improve information sharing. In addition, the method is validated by means of case studies of historical sites in China. In this paper, the historical sites of the Northern Qi Dynasty in Taiyuan, Shanxi, especially the Xuxianxiu Tomb and Lourui Tomb, are discussed in detail. The results indicate that this method is effective for the protection and utilization of historical sites.