Abstract: Species diversity investigation and priority protection evaluation are the basis for the protection of rare and endangered plants. In this paper, the analytic hierarchy process (AHP) was used to build the priority protection evaluation index system. We calculated and analyzed the endangered value, genetic value, species value, comprehensive evaluation value, and the priority protection grade, in combination with the distribution of Cypripedium plants in the upper reaches of Minjiang river, to determine the priority protection areas at various levels. The results showed that the first priority protection species are C. micranthum, C. palangshanense and C. sichuanense. The second priority species are C. farreri, C. franchetii, C. ludlowii, C. debile, C. smithii. The third grade priority protection species are C. fasciolatum, C. fargesii, C. plectrochilum, C. shanxiense, and the fourth priority species are C. henryi, C. bardolphianum, C. guttatum, C. flavum, C. tibeticum. The Wolong Nature Reserve, Huanglong Temple Nature Reserve and Jiuzhaigou Forest Park belong to the class I of priority protection areas, with an area of 275 280 hm² (41%). The Gonggangling Nature Reserve and Munigou Scenic Spot are class II of priority protection areas with an area of 172 022 hm² (26%). The Kalonggou Nature Reserve, Dagu Glacier Scenic Spot, Miyaro Nature Reserve, Jiudingshan Nature Reserve and Caopo Nature Reserve are the priority protection areas of class III, with an area of 225 155 hm2 (33%). The results provided scientific supports for special research and conservation of Cypripedium plants in the upper reaches of Minjiang river.