In the era of post-modernization, profound transformations in urban spaces have led to significant shifts in the spatial composition paradigms of contemporary urban heritage. Research on this process is crucial for elucidating the spatial pathways and compositional changes in the modernization transformation of urban heritage. This study aims to establish identification indicators and assessment systems for the spatial structure of urban residential environments exhibiting historical characteristics and heritage potential through a comparative analysis of residential urban heritage spatial paradigms in historic cities in China and Japan. First, grounded in space syntax theory, this study selected residential urban heritage in Suzhou’s Pingjiang Historic District and Uji’s Nakauji District as research cases. Utilizing road network data, this study analyzed the Life Integration (Int.VR1000) and Global Integration (Int.VR5000) of urban heritage spaces, thereby constructing a spatial topology system for heritage spaces. Second, the study employed urban spatial entropy indicators, such as architectural density entropy, spatial morphology entropy, and function mixing entropy, to quantitatively describe the spatial structure, consequently establishing a heritage space morphological structure indicator system. Finally, spatial clustering methods are used to integrate the spatial topology system with the morphological structure indicator system, resulting in a feature model for residential urban heritage spaces. The research results indicate that the transformation path of residential space paradigms is mainly influenced by spatial topology, affecting the structure of residential heritage spaces in three aspects: functional layout, building density, and spatial form. This phenomenon, in turn, impacts population distribution and the migration of living spaces. However, at the same time, the “resistance effect” of street and lane spaces and the limitations of architectural forms on spatial functions have protected the integrity and authenticity of the internal space.