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Urbanization has been responsible for the loss of cropland worldwide, especially in China. To guarantee national food security, China has implemented a series of policies to protect cropland. One of these policies requires that one-hectare cropland should be reclaimed when urban expansion occupies one-hectare cropland. Since most cropland reclamation leads to a conversion of natural habitat, such as wetland and grassland, urban expansion may lead to (indirect) natural habitat loss in addition to direct loss from conversion of into urban area. While several studies assessed the direct habitat loss resulted from built-up area expansion, few studies investigated the indirect losses caused by cropland displacement. In this paper, a model-based approach is applied to explore both direct and indirect impacts of built-up area expansion on natural habitat loss for the city of Wuhan, China, between 2010 and 2020 using different scenarios. Our scenarios differ in the implementation of strict cropland protection policies and ecosystem conservation strategies. Results show that the indirect loss of natural habitat due to cropland displacement under strict cropland protection policies far outweighs the direct loss due to built-up area expansion alone. Moreover, we found that ecosystem conservation strategies mainly influence the type of natural habitat that is affected, while the total amount of natural habitat loss remains relatively constant.