•Gridded corporate, population, and land-cover datasets were integrated to simulate carbon emissions and sinks at finer geographical scales.•Spatiotemporal variation of intra-city carbon budget and its driving mechanisms were mapped and demystified.•Evaluation indicators and formulating methods for intra-city carbon balance zoning were developed.•Reform suggestions of territorial governance and spatial planning system oriented by carbon peaking and neutrality were generated. Achieving spatiotemporal balance between carbon emissions and sinks at multiple spatial scales is vital for addressing climate change globally. The investigation of carbon budget variation and carbon balance zoning at the intra-city scale, however, has not received much scholarly attention. By integrating firm-level big data with other datasets, this paper aims to simulate high-resolution carbon emissions and sinks and to reveal the spatiotemporal variation of carbon budgets within Nanjing, one of metropolises in eastern China, between 2010 and 2019. We then formulated a carbon balance zoning scheme for 111 township-level regions of Nanjing based on the evaluation indicator system and clustering methods. Empirical results imply that the spatial pattern of carbon emissions has experienced a reshaping tendency from core-periphery to polycentric structure, while the scale and geography of territorial ecosystem carbon sinks remained stabilize during the past decade. There existed a spatial agglomeration effect in functional zones oriented by intra-city carbon balance of Nanjing. These are tied to determinants such as urban expansion, population redistribution, industrial restructuring, as well as regulations on energy use, natural resource supervision and ecosystem protection. The newly built urban sub-centers and new-towns in Nanjing were spatially overlapping with regions where significant changes in carbon budgets occurred. Our findings suggest that the current system of territorial governance should be reformed to support the adoption of major function and carbon balance zoning oriented by carbon peaking and neutrality at finer geographical scales in China.