With the sustained deterioration of marine ecosystems and environment and the improvement of ecological theory, management of the marine ecological redline regions (MERRs) becomes inevitable. We summarize the status and problems of the marine protected areas (MPAs) in China and analyzed the requirements, principles, concepts and system of the MERRs. We suggest that the MPAs and MERRs can be correlated by the similarities in the spatial unity, decision consistency, work contents and management of the objects. The boundary determination, policy decision and management regulation of the MERRs could in respect to the kernel factor, critical factor and important factor of the MPAs. We suggest the methods for the MERRs management at the level of the marine ecosystem, species and habitat. The index system of MERRs zoning can refer to the MPAs selected and evaluated indices. The scale of MERRs, the pattern-structure-process-mechanism of the land-sea ecosystem, combining of complex ecosystem and MERRs, and observation of MERRs base station are the aspects that should be focused on in the future.