The ecological compensation mechanism is a tool for managing regional development and promoting the green economy. This paper proposes a revised model for carbon emissions and absorption based on IPCC, then analyses the spatial and temporal variations of carbon emissions, absorption, and deficit in 31 provinces of China from 2001 to 2019. A model was developed to redistribute carbon deficits and compensate for ecological imbalances, with the aim of eliminating background differences between regions. The concept of ecological compensation sensitivity was proposed, and a redundancy analysis (RDA) was conducted to detect possible influencing factors. Results indicate that: (1) The carbon deficits were relatively substantial in the centre and developed coastal regions, which were the subject regions of China’s ecological compensation. Meanwhile, the northwest and southwest regions were the object regions of ecological compensation, and the compensated object regions tended to extend towards the southeast. The majority of compensated subject areas are generally less sensitive than compensated object regions. (2) The graph of carbon deficit volume over time shows that China’s two carbon targets are closely aligned. The distribution of China’s ecological compensation amounts follows the pattern of provincial economic development levels, with higher compensation amounts concentrated in the central and coastal regions. There is a positive correlation between GDP, year, and population size with carbon emission and carbon deficit. Additionally, there is a positive correlation between year, region, and carbon absorption. (3) This compensation model can strongly incentivise the compensation subject area to proactively adjust its economic development model to cope with the significant compensation pressure. Additionally, it can fully encourage the compensation recipient area to continue adhering to the green economic development model. The conclusions of the study hold significant reference value for promoting the development of a green, low-carbon economy.