Construct a good quality wetland environment for Wu-Jiang estuary, which is very important for developed tourism in Kinmen County. The study adopted system analysis method to conduct the wetland planning of Wu-Jiang estuary. The research site was divided into five sub-systems by the site investigation and analysis results, which are water quality natural purification, wetland ecosystem, vegetation, landscape engineer and management. And the sub-system would include more detail sub-systems, and therefore the system structure and function was uncomplicated. That making the system was easy implementation, and would conform to the objects of construct wetland environment. The estuary wetland was a complex environment. The system analysis system could combine many different disciplines was used to cope with these complicated issues.