To alleviate the pressure of economic development on the marine environment, the Marine Ecological Compensation (MEC) has become a major policy tool for the Chinese government to reconcile the contradiction between economic development and the marine environment. In this paper, we propose a novel two-stage bargaining game data envelopment analysis (DEA) model to evaluate the performance of MEC under the cooperative structure. The proposed model considers the link between marine economic development (MED) and marine environmental protection (MEP). Meanwhile, the equivalent form, Nash equilibrium solution, sensitivity and stability of the model are as well documented to further analyze MED and MEP. Eventually, a case study of 30 coastal cities in China serves to verify the practicable effectiveness of the foregoing model combined with numerical simulation and support key insights as below: (i) According to the results evaluated by the decentralized DEA model, we find that if one party of MED and MEP takes priority, the efficiency score of the other party will be severely affected; (ii) the evaluation results of sensitivity and stability demonstrate that inputs and outputs have different impact degrees on the efficiency scores of MED and MEP, which provide directions for improving the efficiency of both systems; (iii) The proposed model addresses the limitation of the conventional two-stage DEA model that cannot handle uncertain variables, thus revealing the influence of uncertainty on MEC efficiency. The compelling evidence presented in the case study solidifies the effectiveness of the proposed model, establishing its promising prospects for application in evaluating the performance of DMUs with a two-stage structure.