As a dominant function in ecosystem, biodiversity has key roles at the ecosystem service hierarchy. Quantification and valuation of the biodiversity service is a critical basis of the ecological protection decision-making. Based on the average willingness to pay of residents for maintenance of rare and the endangered species, the biodiversity maintenance value of the Yellow Sea were estimated from 2002 to 2012. The results showed that the willingness to pay of citizens for maintenance of 17 rare and the endangered species of the Yellow Sea presented a rising trend year by year. By 2012, the total willingness to pay for the 17 species was 9706 billion yuan, with the highest percentage from Shandong province (45.75%), which has increased by 247% compared to that in 2002. The per capita willingness to pay for maintenance of the 17 rare and endangered species of the nine cities along the Yellow Sea was between 121 and 259 yuan. Qingdao toped the list of the per capita willingness to pay, followed by Yantai and Nantong. The biodiversity maintenance value of Saccoglossus hwangtauensis, Grus vipio and Grus japonensis were the highest of the 17 species, more than 0.8 billion yuan each. The results provide scientific basis and theoretical support for protecting and developing of the Yellow Sea biological resources.