The progress of human settlement research in geography and architecture is reviewed from the perspective of a theory tree. First, an exploration of the research skeleton indicates that the two disciplines have the same tree roots, that is, nine research subjects and eight research scales; the same tree trunks, that is, nine research subjects and eight research scales; and the same tree branches, that is, 33 research fields; however, they have different tree leaves, in other words, there are different quantities of research achievements in each research field. Second, a comparison of the characteristics of the research achievements indicates that the research achievements in the two disciplines differ significantly. For six secondary subjects (e.g., suitability), there are abundant research achievements in geography, but few in architecture. For six secondary subjects (e.g., planning) and the architectural scale, there are abundant research achievements in architecture, but few in geography. For twelve secondary subjects (e.g., spatial pattern) and six scales (e.g., city), in both disciplines, there are abundant research achievements, but the focus points of their research achievements differ. For the behavior of the secondary subject and global scale, in both disciplines, there are few research achievements, but the focus points of their research achievements differ. Finally, the generative logic of the difference in achievements between the two disciplines is analyzed, and future interdisciplinary research pathways are proposed. The logical starting point for different achievements is due to different discipline categories. The logical chain of the difference in achievements is the transmission mechanism of "discipline categories-discipline characteristics-researchers-research preferences-research paradigms-research achievements". Among them, the difference between research paradigms is an important link in the chain. In the future, human settlement research paradigms should be improved, including extending the research framework, developing research subjects, planning research scales, applying multisource data, and using mixed research methods. Moreover, there should be a response to the needs of real-world development in terms of globalization, beautiful human settlements, emergencies, and interdisciplinary cooperation.