On the occasion of the reform of natural protected areas management system, the management effectiveness evaluation helps to identify the threats and pressures of the protection and determine the priority of protection management. Combined with the conditions of Fujian Province, this research optimized evaluation index system of the Rapid Assessment and Prioritization of Protected Areas Management (RAPPAM) methodology and evaluated the management effectiveness of 53 protected areas in 9 prefecture-level cities, in order to identify the main pressures and threats and analyze the advantages and disadvantages of protection management. With Spearman's correlation analysis, the relevant management steps were identified to lessen the threats, which provided priority adjustment reference for the protected areas management in Fujian. The results show that:(1) the main threats and pressures are successively fire, breeding, pests, environmental pollution and tourism, in which the last two have the most serious impact; (2) the management system of Fujian natural protected areas is at the medium level with regional differences. There are widespread problems, such as multiple management, insufficient management input, and lack of management implementation plans. (3) From Spearman's correlation analysis, the improvement of the management and input in the protected areas can help reduce the threat of fire, pests, breeding. And environmental pollution and tourism threats are significantly affected by macroeconomic development, the planning of protected areas and surrounding lands.