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Objectives: Few studies have examined the impacts of structural differences in the urban–rural dichotomy under the new household registration policy on migration and settlement behavior. Nevertheless, the rationale for the settlement policy of local governments should be further elucidated and improved. This study aims to analyze the household registration, land property rights, and differences in migrants’ settlement intentions. Methods: This study used migration survey data from the Pearl River Delta and probit regression to fill this gap in the literature. Findings: Because of the long-term effects of the household registration system and their socioeconomic differences, urban-urban migrants and rural–urban migrants differed in their settlement intentions. Furthermore, the new points-based household registration system affected migrants’ settlement intentions. Relative to the rural–urban migrants, urban–urban migrants more easily met the settlement requirements under the points-based system, and they tended to settle in their current cities. By contrast, migrants with farmland in their hometowns tended to settle there. The findings underscore the relevance of adopting perspectives that consider the urban–rural dichotomy and related structural differences to understand migrants’ settlement intentions in China.