Aquaculture exists universally in marine nature reserve (MNR). The government and relevant interest group pay close attention to the coordination between the protection and aquaculture. Based on the types of protected targets and the status of aquaculture activities in our national marine nature reserves, we analyzed the potential eco-environmental impacts of aquaculture on MNR from the protected targets and the aquaculture methods. We found problems such as inconsistent management policies for aquaculture in MNR, lack of relevant MNR contents in management policy for aquaculture by combing through aquaculture management and sea using policy. Therefore, in combination with a series of policy documents on nature reserves in the new era, we put forward four management suggestions, including refining the aquaculture management requirements in MNR, carrying out the pilot project for the aquaculture management in MNR, strengthening the management coordination among the MNR, marine areas and fisheries, and strengthening the management capacity building of MNR. These suggestions may provide references for the management of aquaculture in China’s MNR, promote the coordinated development of MNR and surrounding fishing communities.