China has been working for nearly four decades to establish marine protected areas (MPAs). After the 2018 institutional reform, all the protected areas were integrated into a unified management by the Ministry of Natural Resources. Therefore, it is urgent to summarize management experiences and put forward new management countermeasures. In this study, we analyzed the development process of China's MPAs and show that, after a long-term increase, both number and area of newly built MPAs shrank after 2008. No-take marine nature reserves used to largely contribute to the MPA network. However, because of the shortage of land for economic development, willingness to build nature reserves in coastal areas, as opposed to reclamation and other marine exploitations, was relatively low nationwide in the last decade. Thus, marine special protected areas, which were smaller and with multiple-use strategies, became more important. Top-down decision-making process, decentralization, and unbalanced spatial distribution are the main challenges hampering an effective MPA network. In China, a unified jurisdiction of MPAs was implemented after institutional reform, which made a new top-level design possible. Appropriate categorization consisting of fully protected and multiple-use MPAs, a balanced system integrating top-down and bottom-up approaches, and a flexible and adaptive MPA network are suggested to achieve sustainable development of China's MPAs.