Abstract: Main functional zone (MFZ) planning is one of the most important national strategies in economic development and ecological environment protection. It is very necessary to analyze the evolution characteristics of territorial space patterns and the carbon emission in the MFZ system. This study aims to determine the spatial and temporal evolution of territorial spatial patterns in the Yangtze River Delta region before and after the MFZ implementation using the land use data from 2000 to 2020. The spatial transfer of territorial space was then evaluated using carbon emission data and contribution rate analysis. The results show that: 1) Urban and ecological space continued to increase, whereas, the agricultural space decreased in the study area. The agricultural main production, the optimized and the key development zones were dominated by the transfer of agricultural production space, while the ecological function zone was dominated by the mutual conversion of forest ecological space and agricultural production space. The rate of change in the territorial space tended to slow down after the MFZ implementation. 2) Agricultural production space was the main type of transfer out, whereas, the transfer in was the agricultural living space, urban living space, and urban production space. There was a negative correlation between the increase and decrease in the number of spatial changes in the territory within each MFZ, indicating the significant spatial heterogeneity. 3) Net carbon emissions decreased (in C units) by 14956.57 kg/(m²·a) with a spatial distribution of high in the west and low in the east. Among them, the high-value areas were clustered and distributed in the key development zones and the agricultural main production zone. Regional agglomeration was enhanced by the net carbon emissions enhancement in the key development and ecological function zone. The reduction zone was distributed mainly in the main production areas of agricultural products. There was an increase in the number of carbon emissions that converted to carbon sinks on the grid scale after the MFZ implementation. 4) The reduced net carbon emissions were attributed to the conversion of agricultural production space into forest ecological space. There was a decrease in the carbon emissions in other main functional zones, due mainly to the conversion of agricultural living space to agricultural production space. Furthermore, the conversion of agricultural to urban space was attributed to the increase in carbon emissions in each subjective functional area. A diversified type of territorial space was attributed to the variations in the carbon emissions after the implementation of the MFZ planning. As such, the MFZ system should be further improved to reduce carbon but increase sinks in the territorial space. Territorial spatial planning should be compiled with the local conditions in low-carbon-oriented activities. Therefore, green and low carbon utilization can be realized with the goal of reducing carbon and increasing sinks in the territorial space.