The willingness to pay (WTP) for marine conservation is an important basis for the design of market-based marine protection strategies and sustainable marine environment development. Whether the individual was willing to pay and how much they would prefer to pay may be affected separately by different factors. Thus, we investigated the probability of paying for marine conservation and the payment amount to obtain evidence regarding the factors that influence the preferences of stakeholders. We considered two marine protected areas in Zhejiang Province, China, where we combined contingent valuation with logit and tobit models to measure the differences in the WTP for marine conservation between tourists and residents. The results showed that most respondents were willing to pay for marine conservation, but they were affected by different factors. The average amounts that the respondents were willing to pay were 216.20 CNY ($34.3) and 172.43 CNY ($27.4) in the Nanji Islands MPA and Putuo Islands MPA, respectively. The probability of respondents’ WTP was closely related to their individual environmental awareness, whereas the payment amount was influenced mainly by personal income. Thus, our results suggest that increasing human environmental cognition and developing differential payment schemes for the marine environment among stakeholders may promote sustainable marine protection development and management.