Abstract: The value of the biodiversity perceived by the stakeholders will influence their behavior and attitude towards environment protection and thus impact the efficiency and effectiveness of policies related to environmental conservation directly. To characterize the value perception of biodiversity by stakeholders in a specific region more accurately, a method of choice experiment designed from the perspective of flagship species was proposed. The steps of the method included: selecting flagship species for attribute design based on the study area, optimizing and generating the choice experiment questionnaire for the formal survey based on the results of the pre-survey, obtaining the willingness to pay through the questionnaire survey, evaluating the value of biodiversity in a specific region. Applying the methodology in Qinling Mountains (Shaanxi section), giant pandas, golden monkeys, and crested ibis were selected as flagship species, and 1 288 individuals were finally included through field visits and online surveys. The results showed that the marginal monetary willingness to pay of respondents from inside and outside Shaanxi Province for Qinling biodiversity protection was 146.29 and 212.60 yuan per year, and the value of marginal time willingness to pay was 240.12 and 350.01 yuan per year, respectively. According to the marginal willingness to pay, the biodiversity value of Qinling Mountains (Shaanxi section) was estimated to be 489.772-979.545 billion yuan per year. The case study proves that this method can reflect the value of biodiversity in a more comprehensive and comprehensible way, and provide a solid data basis for the formulation and implementation of ecosystem protection policies.