Due to fast urbanization, natural ecosystems are increasingly being replaced by urban development. Human health is also being threatened. Shanghai has been experiencing a rapid urbanization for over two decades. It is challenging to protect the unique natural ecosystem for planners and decision makers because of the complex ecosystems and other factors. This paperpresentsan integrated method for planning urban land-use by combining HHM (habitat heterogeneity model) and MCA (multi-criteria analysis) with GIS. The authors evaluated the suitability of this method for four types of land usage including nature reserves, forest plantations, residential areas and industrial areas by taking Shanghai, China, as the study area. Factors considered in the model were soil characteristics, topographic attributes, vegetation cover, human population density and landscape heterogeneity. Results indicated that central city ismost suitable for residential areas. Nature reserves and forest areas are mainly distributed in the three islands of Chongming County and southern, northwestern and southwesternparts of Shanghai. The industryarea is best located in the eastern city. The success of this method in Shanghai can be copied to other developing cities in China. In order to provide a scientific basis for ecological conservation and biodiversity protection during urban development, we propose to establish a technical guidance principle on urban planning and a relatively uniform evaluation system.