Carbon cycle is a key link affecting climate change. In this paper, the improved CASA model is used to estimate the natural carbon sources and sinks in Northeast China during 2000-2020. By adding the constraints of real carbon emissions in the estimation process, we improved the estimated methods of the energy consumption carbon emission. The spatial and temporal distribution and influencing factors of regional carbon sources, carbon sinks, and carbon sequestration were investigated. The results show that:(1) in terms of time, the net ecosystem productivity fluctuated and increased. In terms of space, Heilongjiang Province had the highest total natural carbon sink (164.61 Tg C/a), accounting for 60% of the Northeast China. (2) The total carbon emissions from energy consumption rose firstly, then declined, and tended to be stable in recent years. Liaoning Province had the fastest annual growth rate of carbon emissions, which was about 6.95 Tg C/a. (3) 2005 was the turning point for the three Northeast provinces from carbon surplus to carbon deficit, and the rate of carbon deficit decreased in recent years. (4) The carbon surplus and deficit of Northeast China showed positively correlated with natural factors, which presented negative correlation with the total population, gross regional product, carbon emission intensity, and industrial structure. The increase of total energy consumption in Liaoning Province made the decline of energy structure fail to reverse the situation of carbon deficit, and made the carbon deficit and energy structure to present a positive correlation. The rapid loss of agricultural population in Heilongjiang Province and Jilin Province resulted in a positive correlation between urbanization level and carbon deficit. (5) The Northeast China should all reduce carbon emission intensity, Heilongjiang and Jilin should adjust their energy structure, while Liaoning should adjust its industrial structure. The rapid loss of agricultural population in Heilongjiang Province and Jilin Province resulted in a positive correlation between urbanization level and carbon surplus and deficit. The research results can provide a theoretical basis for the realization of the carbon peaking and carbon neutrality goals in the three northeastern provinces.