As ecosystem services becoming the ad hoc to researchers, their spatial pattern and relationship with biodiversity also have been kept focus on. Existing studies showed that ecosystem services conservation were not considered in reserves planning, which largely aimed to protect biodiversity. Based on GIS, this study mapped ecosystem services in Huanghuaihai region through horizontal and longitudinal dimension (2D), as well as added vertical dimension (3D), and recognized key ecosystem services area. Then the spatial congruence between ecosystem services with biodiversity was tested and analyzed. Results shown existing wetland natural reserves have little ability to capture key ecosystem services area, and there are lots of important key ecosystem services gaps. The spatial congruence between them suggested that 3D is more practical than 2D to key ecosystem services protection, which is similar to hot area in conservation biology. So the systematic conservation planning theory could be introduced to ecosystem services protection in the future, integrating them together as conservation target.