Regional carbon emission accounting is one of the core concepts of current global climate change and carbon emission research. The development of regional coordination which has always been the focus of attention, and the importance of both the ecological environment and policy fairness is the central study for all kinds of land use planning. In 2010, China published the national functional zoning plan, which is based on regional development, resource environment foundations, and future development potential. According to the plan, the county is the basic unit of the regional carbon emission planning programs, which provides a new perspective for regional carbon accounting and quota allocation. Because the energy data for counties was not sufficient, this study has developed a new carbon emission accounting method based on the economic, population, and provincial energy consumption data, which is suitable for the division of main functional areas. We used the carbon intensity of three industries and per capita carbon emission as the main indicators to calculate the emissions. This method ensure two conditions:the total amount of carbon emissions of main functional areas should be equal to the carbon emissions of the province, and the carbon emissions of main functional areas in four sectors should be equal to the carbon emissions of the province in the corresponding sector. By taking Guangdong Province as a case example, this paper accounted for and analyzed the carbon emission of the four main functional areas of Guangdong Province from 2005-2015.The analysis reveals that the total carbon emission of the four main functional areas is highly positively correlated with their total economic output, but the GDP growth rate will be slightly higher than the carbon emissions growth rate on the whole. There is a link between "economic growth-energy consumption-carbon emissions" in the research results. The largest carbon emissions in the four regions was the optimizing development zone, which accounted for 64.84% of all emissions in 2015. The second largest emissions was caused by the key development zone, which account for 21.04%. The largest carbon emission intensity was the ecological development zone, at about 1.89 t/10000 yuan. The second highest carbon emission intensity was found to be in the key development zone, and next was the agricultural development zone. The optimizing development zone has the lowest carbon intensity because of its advanced economic development. The optimizing development and key development zones should be served as the main targets for future energy conservation and emission reduction measures. The optimizing development zone should speed up the application of new energy technology and accelerate industrial upgrading. The agricultural development and ecological development zones should develop more environmentally friendly industries, such as organic food, low-carbon agriculture, and ecological tourism.