Dynamic monitoring and evaluation of regional carbon budget is a key and basic problem for promoting the low carbon development and carbon peak in urban agglomeration. It proposed and analyzed the spatiotemporal coupling relationship between regional carbon budget and urban spatial morphology in the Yangtze River Delta urban agglomeration. Firstly, based on the carbon emissions, net primary productivity, land use and soil data in 2001, 2005, and 2010, the spatiotemporal distribution estimation model of carbon budget in the Yangtze River Delta urban agglomeration was constructed. Then, the correlation between landscape pattern indices of urban spatial morphology and carbon budget was analyzed with the geographical weighted regression model. Finally, the influence of landscape pattern index factors on carbon budget and their interaction was quantitatively analyzed by geographical detector. The results show that:(1) the carbon budget of Yangtze River Delta urban agglomeration presents obviously spatial heterogeneity, which is higher in the south of the urban agglomeration, followed by the north and lower in the east; (2) The carbon budget of Yangtze River Delta urban agglomeration also presents obviously temporal heterogeneity, showing a decreasing trend from 2001 to 2010 with a large decline from 2001 to 2005; (3) The area of patch type, the number of urban patches, the maximum patch index, and the landscape shape index are negatively correlated with carbon budget while edge density, urban built-up area patch density and carbon budget have significantly positive correlation; (4) The total built-up areas in 2001, 2005 and 2010 are the main driving factors for the spatial heterogeneity of carbon budget; the interaction between patch type area and other factors contributes more to the spatial heterogeneity of carbon budget than others. This paper reveals the correlation between landscape pattern indices of urban spatial morphology and spatiotemporal distribution of carbon budget, which can provide scientific reference for carbon peak/carbon neutralization and urban morphology optimization, etc.