Ecological rehabilitation plays an important role in ecological civilization construction of China. On the basis of related concepts of ecological rehabilitation, the public goods attributes owned by ocean and the externalities in the utilization of marine resources, the paper divides marine ecological rehabilitation into indemnificatory marine ecological rehabilitation and compensatory marine ecological rehabilitation from the perspective of the internalization of the externalities of public goods governance. Then, the study explores four main aspects according to the above classification of marine ecological rehabilitation:the subject of marine ecological rehabilitation, rehabilitation standards, rehabilitation approaches, and rehabilitation measures. According to our analysis, four main findings are listed as follows. In terms of the subject, there is a specific subject with mandatory and clearly defined responsibility in indemnificatory ecological rehabilitation, which makes it easy to trace the responsible subject in case of some issues occurring. By contrast, it is hardly possible to identify the clear responsibility subject for rehabilitation in compensatory ecological rehabilitation. Under this circumstance, the government should undertake the ecological rehabilitation project aiming to compensate for the public interests and increase social welfare. In aspects of rehabilitation standards, as the subject of indemnificatory marine ecological rehabilitation, marine resources users, who pollute and destroy marine environment, should calculate the rehabilitation scale and rehabilitation costs based on the Habit Equivalency Analysis or the Resources Equivalency Analysis. Compared with the above, the government, as the subject of compensation-based marine ecological rehabilitation, could incorporate ecological rehabilitation into the marginal analysis framework of traditional economics and determine the optimal rehabilitation scale in accordance with marginal cost-benefit analysis. As far as rehabilitation approaches, following the principle of "who damages, who rehabilitates", marine resources users shall adopt the command-controlled rehabilitation method or appoint a third party to repair the damaged marine ecosystem (economic incentive repair mode), so as to restore the damaged marine ecology to the baseline level before the destruction. The government should adopt economic incentives such as government procurement and creating market potential for marine ecosystem restoration in order to increase social welfare. In the last part of the study, due to the fact that marine ecological rehabilitation in China is a relatively new field for environmental protection, there are still some urgent problems to be solved and improved in the construction of the marine ecological rehabilitation system. Great importance should be attached to the financial guarantee and supervision systems of ecological rehabilitation, R&D of ecological rehabilitation, and cost-benefit evaluation after ecological rehabilitation.