The development of marine protected areas faces an important transformation. It no longer emphasizes area and quantity but greater attention is paid to construction and effectiveness. Thus, marine protected area management is under tremendous pressure. As an important means to evaluate the degree of realization of protected area management objectives, management effectiveness evaluation of marine protected areas, especially coastal wetland protected areas, has recently received attention from ecologists at home and abroad. Relevant theoretical research and research on methods of construction and application practices have been conducted successfully. At present, most of the assessments of marine protected areas in China draw on mature foreign systems, failing to fully consider the special characteristics of the local oceanic environment, and related domestic research that still needs to be implemented. Based on the problems existing in the current evaluation system and the characteristics of construction and development in the Guangxi coastal wetland nature reserve, the evaluation framework of "management mechanism-management foundation-management behavior-management effectiveness" was developed, and an indicator system was designed using consultation methods and an analytic hierarchy process (AHP), including 4 elements, 19 assessment indicators, and 6 additional indicators. The following four are characteristics of this assessment system:(1) Unlike administrative supervision and inspection, the various output benefits of the protected area management system were considered comprehensively and included control, ecological, social, and economic effectiveness. (2) The indicator design takes into account the habitat characteristics of the coastal wetland nature reserve and the willingness of managers and the public to protect it. (3) To minimize the influence of subjective factors, quantitative work, such as weight setting, grading assignment, and percent distribution, was applied to the indicator system. (4) Assessment of indicators, such as changes in ecological environment quality and landscape, in protected areas requires long-term effective statistical data. This evaluation system is applicable to the coastal wetland type protected areas system with effective monitoring. Finally, the national nature reserve of Guangxi Beilun estuary was used as a research area for verification of the evaluation system. The evaluation results showed that (1) the case area evaluation index score was 78 points with an additional 3 points, for a comprehensive evaluation score of 81 points, and its management level was level II, indicating that the protection management achieved good results. (2) The score ratio of each factor was ranked as follows:C Management Behavior (100%) > A Management Mechanism (90%) > B Management Foundation (87%) > D Management Effectiveness (65%), and the proportion of the number of evaluation indicators at all levels was I (53%) > II (21.05%) > III (16%) > IV (11%). (3) The score ratio of the 3 types of management effectiveness was D₂ Control effectiveness (97%) > D₁ Ecological effectiveness (60%) > D₃ Social and economic effectiveness (35%), thus, indicating that the ecological effectiveness of the case area was generally good, although the social and economic effectiveness was poor. Based on this analysis, the main problems faced by case area management were discovered and included insufficient technical capabilities, weak talent team building, and diverse human intervention. We recommend that protected areas should strengthen capacity building and control, strengthen public awareness, promote community co-management, pay attention to the protection of ecosystems other than mangroves, and promote regional sustainable development.