Located in the eastern coastal areas of China, featured with vast area of wetlands and rich biodiversity, HuangHuaiHai Region (HHHR) is an important place for migratory birds to survive during migration and wintering not only for China, but also for Northeast Asia Inland and Western Pacific Rim, which is a vital component of East Asian-Australasian Flyway. By applying basin units rather than administrative districts to account for the connected nature of wetlands, the study area of HHHR was defined, mainly made up of alluvial plain deposited by Yellow River, Huaihe River, Haihe River and their tributaries, covering an area of approximately 48000000 km². As the political, economic and cultural center of China, with about 4 times population density of the national average, wetlands within HHHR not only played very important role in providing huge suitable habitats for various wildlives and great ecosystem services for local people, but had long been suffering from large-scale destruction and increasing degradation during the half past century. How to keep economy sustainable development while guarantee eco-conservation as well, multi-scenarios analysis based on Systematic Conservation Planning (SCP) should be the effectual tool in decision-making. Therefore, within the framework of SCP, taking catchments as planning units, considering comprehensively biological information (such as 23 riverine wetlands ecosystem types, 8 non-riverine wetlands ecosystem types, distribution of 16 target species prioritized on IUCN Red List, 5 exploitable aquifers) and socio-economic factors (such as road nets, settlement places, dams), also with existed reserves concerned, based on 2D connectivity (lateral connectivity, longitudinal connectivity) and 3D connectivity (lateral connectivity, longitudinal connectivity, vertical connectivity) respectively, multi-scenarios for wetlands ecosystem conservation in HHHR were simulated firstly, then followed by scenarios comparison under different targets and compactness to develop the reasonable conservation planning. Eventually, by taking planning units selected (pus) per cost as conservation efficacy (e), conservation planning of 2D connectivity was paralleled with that of 3D connectivity. The main conclusions are as follows: As to development of conservation planning based on 2D connectivity, 30% target set for riverine wetlands, non-riverine wetlands and species was proposed, compactness of conservation pattern should be better when the value of Boundary Length Modifer (BLM) was 0.36. However, when referred to 3D connectivity, target set of 30% for riverine wetlands, non-riverine wetlands and species, and 55% for groundwater, with the BLM value of 0.06 for compactness was relatively suitable. When it comes to the comparison of 2D connectivity with 3D connectivity, although the cost of conservation planning under 3D connectivity was more than that under 2D connectivity, while the pus under 3D connectivity is far more than that under 2D connectivity, both increasing as targets increased. In addition to that, the conservation planning of 3D connectivity was more efficient than that of 2D connectivity on the whole, because more wetlands could be protected per cost under 3D connectivity conservation planning in contrast to 2D connectivity's. Finally, it's obviously that constructing wetlands conservation system based on 3D connectivity was not only necessary, but also possible, which was of great practical significance, especially for HHHR.