In the large scale map of urban area, obvious difference in geometric position often tend to exist in multisource habitation data, which increases the difficulty and uncertainty of habitation matching. A new matching method for areal habitation by using the skeleton line mesh of blank region is proposed to solve the above problem. Firstly, the one-to-one mapping relationship between skeleton line mesh and habitation is established based on skeleton line network of blank region so that the matching object is transformed from habitation to skeleton line mesh. Secondly, the dual graph of skeleton line mesh is constructed by the connective topology, and the centrality indexes of each node in the dual graph can be calculated. Then the matching model of skeleton line mesh is established by polarization transformation and analytic hierarchy process, accordingly the matching results of skeleton line mesh can be obtained. Finally, the matching results of skeleton line mesh can be transformed into habitation matching results by the mapping relationship. The transformation of matching object, dual graph construction and polarization transformation of the skeleton line mesh can add the constraint conditions of topology and relative position to the matching process, so that the influence on matching caused by the obvious geometric position difference can be reduced significantly. Comparison experiments and analysis with other areal matching methods indicate that the proposed method can solve the matching problem among the areal habitation data of the large scale urban map with obvious geometric position difference effectively.