On the basis of summarizing the connotation of ecological protection compensation (EPC) and taking into consideration the policy objective, the nature of marine environments, the particular characteristics of nature reserves, as well as China's institutional context, the guideline of Ecological Protection Compensation Mechanism in Marine Nature Reserves (EPCM-MNRs) was developed. In accordance with the relevant laws and the ecosystem services analyses on typical Marine Nature Reserves (MNRs), the subjects, objects, and compensation standards of EPCM-MNRs were discussed. The results show that, EPCM-MNRs should aim to continue the sustainable supply of ecological benefits with the fundamental principle that internalization of positive externalities. The subject of EPCM-MNRs is the central government, some government departments should be as agents of the central government to fulfil the obligations of ecological protection compensation. The objects of EPCM-MNRs are the residents living in or around MNRs, and the administrator of MNRs. Compensation standards for the residents depend on the value of the ecological benefit they forfeited for the MNRs. Compensation standards for the administrator of MNRs depend on the value of increased ecological benefit, which is provided by MNR ecosystems under their management. Finally, based on the framework of the EPCM-MNRs, funding support for the operation of MNRs, and the credibility of compensation standards were discussed, providing a foundation for further research and practice.