Wetland assessment has been a popular field of research worldwide. However, various indicators have been used in wetland assessment for different purposes and backgrounds and also because of the research limitations. Therefore, a more comprehensive, sound, and efficient indicator system is needed for researchers’ referencing to evaluate wetlands. After an extensive review of wetland assessment literatures, the reported indicators were evaluated using the developed assessment system, based on the Analytical Hierarchy Process (AHP) with three main goals: nature protection, function utilization, and sustainable development. Each indicator was evaluated using two methods. The first method was to study the percentage of the indicator application, and the second was to assess the weighted ratios assigned to the indicators according to principles of comparability, typicality, sensibility, and availability. The results of these two methods were compared to study the commonalities and specialties of the indicators. They also showed that some indicators were widely used, including biodiversity, weather and climate, hydrological change, and the output of wetland. On the other hand, other sustainable indicators were easily ignored, such as environmental carrying capacity and wetland planning. Furthermore, an indicator system for wetland assessment was structured and strategized to discuss how to choose indicators for wetland assessment under different conditions. The proposed approach can be used to guide the process of wetland assessments in the future.