This study investigates the spatial–temporal patterns of urban morphology in three dimensions and their impact on the Malaysian heritage cities of George Town, Malacca, and Brickfields Little India. The study identifies key morphological patterns and their implications for urban heritage by examining historical cases. Engaging a combination of geospatial analysis, historical mapping, and case studies, this research examines the evolution of urban form over time and its implications for heritage urban design, functionality, and physical and social changing aspects. Findings reveal significant shifts in land use, activities, building density, public space, and street space configuration. These changes have a perception of heritage space, and its identity and altered pedestrian flow, vehicular traffic, and the overall functional and visual quality of the heritage space. The morphology of the building has an impact on the activities around it. The study highlights the need for sustainable heritage urban design strategies that balance development with the preservation of cultural, heritage, and environmental assets, ensuring that the unique character and identity of Malaysian heritage are maintained while enhancing its infrastructure and liveability. Through this case study, understandings are provided into the challenges and opportunities associated with balancing urban development and urban heritage in rapidly growing Malaysian cities.