Since the 1980s, China has experienced an unprecedentedly rapid urbanization process, during which the historical environment of many cities has been damaged to some extent. Accordingly, the fragmented historical environment poses great challenges to the protection of the city’s overall historical form and inheritance of cultural context. The interactive relationship between man and nature formed in the process of urban evolution and the form of life supported by it constitute the implicit structure of historical environment. However, as a means by which historical culture influences urban construction, the implicit structure of historical environment has been easily neglected in previous studies. Taking Xuzhou as a case study, this paper studies how the concept of “the Harmony Between Man and Nature” influences the formation of urban historical environment structure. The research methods employed are literature analysis, field investigation, mapping analysis, classified statistical analysis, and schema analysis. From the three dimensions of natural landscape, underground space, and age-old historical buildings, this paper reveals the form and characteristics of implicit structure of historical environment formed in the interaction between urban construction and natural environment. The results show that the natural landscapes of Xuzhou serve as the foundation and core characteristics of the formation of Xuzhou’s historical environment; underground space and age-old historical architecture can trace the long history of city development and reflect the overlapping spatial marks of different ages. Based on the characteristics of Xuzhou’s implicit structure of historical environment, the paper explores the possibility of guiding urban renewal based on such aspects as form control, resource integration, and multi-cultural display. Hopefully, this study is of some help to achieve the balance between and fusion of modern construction and historical inheritance in urban renewal.