Predicting the change in carbon storage in regions of high carbon uptake and those under highly intensive human disturbance is crucial for regional ecosystem management to promote sustainable development of the economy and ecology in the future. We use a process‐based model to estimate the terrestrial carbon storage in Yangtze River Economic Belt (YREB) and to predict the change of carbon storage over the next 100 years. The results show that the vegetation carbon (VC) and soil organic carbon (SOC) storage were 8.97 and 28.85 Pg C in the YREB from 1981 to 2005, respectively. The highest VC density is distributed in the southern region of the YREB, and the highest SOC density distributes in subalpine and alpine area of the western region of the YREB. Carbon storage in the YREB continued to increase from 1981 to 2005 and in future projections, under both the representative concentration pathway 4.5 (RCP4.5) and the RCP8.5 scenarios. The increased rate of carbon storage in the YREB under the RCP8.5 scenario is higher than that under the RCP4.5 scenario. Under the RCP4.5 scenario, the increasing trend of VC storage tends to be reduced after the 2060s; conversely, the increase of both VC and SOC is accelerated after the 2050s under the RCP8.5 scenario. The SOC density in Western Sichuan will decrease in the future, especially under the RCP8.5 scenario. Western Sichuan has the highest SOC density in the YREB; therefore, it is important to manage the ecosystems there in order to cope with significant warming. The positive impact of warming and the CO2 fertilization effect on vegetation growth and carbon uptake will be predominantly attributed to the increase of terrestrial carbon storage in the YREB. However, warming will stimulate the decomposition of soil organic carbon, contributing directly to reducing SOC storage in high‐altitude regions (e.g., alpine and subalpine regions of Western Sichuan).