When responding to contingent valuation method (CVM) valuation questions, some respondents may show uncertainty in their willingness to pay (WTP) because of the lack of cognition of the goods to be estimated, which will cause uncertainty bias. This study took the valuation of marine biodiversity in Pingtan County, Fujian Province as an example, to identify and correct the uncertainty bias by adding follow-up questions and incorporate uncertainty into the framework of WTP estimation, which will reduce the bias and improve the validity of CVM. The results show that about 50% of the respondents were uncertain of their willingness to pay, which means that the uncertainty could be universal. Years of residency in the area, knowledge of marine biodiversity, and income had significant effects on the uncertainty. Incorporating uncertainty into the estimation of WTP, the parameter estimation results show that the estimated WTP to preserve marine biodiversity was RMB 200.24 yuan per person each year and the value of marine biodiversity in Pingtan was RMB 88.89 million yuan per year. The conclusion may deepen the understanding of the sources as well as the correction methods of uncertainty bias, and thus improve the validity of estimation results in CVM and provide data support for the protection and governance of marine biodiversity in island ecosystems.