Huangpu ancient port and Huangpu village are geographically continuous, located in Shiji village, Pazhou street, Xingang east road, Haizhu district, Guangzhou city. The ancient port was already “the place where sea vessels gathered” in the Southern Song dynasty, witnessing the prosperity of the “Maritime Silk Road”, and is now an important representative of spatial governance for urban renewal, cultural heritage preservation and transformation of urban villages along the Pearl River. This work explores and designs the material entity composition and practice path of spatial governance in and around Huangpu ancient port from the perspective of spatial governance: elements - levels - culture - value - practice and its logical relationship of spatial governance. First, we summarize the problem based on the material elements of the village entity, and extract the elements from the macro urban design positioning, meso traditional village protection planning, and micro spatial utility transformation to summarize. Second, based on the analysis from point to line to network to surface, we clarify the identification and integration of traditional village elements, hierarchical classification and structural optimization, cultural extraction and sublimation, value enhancement and inheritance development, and the implementation path of multi-layer comprehensive governance. Thirdly, we designed specific nodes from the perspective of multiple participant subjects, multi-layer practice sequences, and full cycle, and clarified the interactions between “land-land” and “people-land” relationships.