Carbon sequestration service provided by terrestrial ecosystem can mitigate climate change by directly absorbing atmospheric CO2. The balance between the supply and demand of carbon sequestration service is crucial for sustainable development in urban areas. However, spatially explicit and quantitative investigation of the changes in the supply and demand of this ecosystem service is relatively rare. In this study, the CASA model was adopted to measure the net primary productivity to represent the supply of carbon sequestration service. Meanwhile, the IPCC Guideline Inventory as well as the carbon metabolism method were used to measure the anthropogenic CO2 emissions to represent the demand of carbon sequestration service. Then, the balance of the supply and demand of carbon sequestration service in 2000 and 2013 were analyzed. The results showed that the supply of carbon sequestration service in 2000 was in short, the overall supply/demand ratio being 53.5%. Spatially, the demand of the service was far beyond the supply of the service in the central districts whereas the situation was opposite in the northern and western districts. In 2013, the gap between the supply and demand of the service was even larger that the supply/demand ratio dropped to 38.5%. Spatially, the gap between the supply and demand was widened in the central districts. The widened gap was mainly due to the increase in CO2 emissions accompanying with urbanization process. Specifically, CO2 emissions from household use and transportation contributed most to the increase. Therefore, it is highly recommended to enhance ecological conservation, improve the efficiency of energy consumption and accelerate the transformation of industrial structure for a more sustainable development path in Beijing.