Abstract: Sacred Natural Sites (SNS) are defined as areas of land or water having special spiritual significance to indigenous peoples and communities. SNS is considered the earliest form of protected area in the world. The spatial pattern of SNS in Three-River-Source National Park embodies the typical landscape features of Three-River-Source Area and its cultural system reflects the cognitive tradition of the local Tibetan people to the landscape. Based on literature research, field investigation, and semi-structured interview and mapping, this research identifies the cultural system, spatial pattern, and behavioral tradition of SNS, and recognizes herdsmen’s cognition towards the above three aspects. It reveals the multiple values of SNS of Three-River-Source Area, as the indigenous living and belief space, unofficial protected area, and visitors’ leisure space. It also discusses changes in the natural and cultural environments, increasing ecological impact, lack of management, among other problems in SNS, which are caused by the climate change, social transition, indigenous lifestyle change, and increasing visitor activities. Under the background of China’s national park system construction, this research puts forward some suggestions on the identification, research, and conservation of SNS in Three-River-Source National Park.