[Objective] The dynamic changes in vegetation carbon use efficiency (CUE) and its relationship with hydrothermal factors in the Inner Mongolia Autonomous Region was investigated to provide a scientific basis for evaluating vegetation carbon sequestration capacity. [Methods] Vegetation CUE was calculated using MOD17A2H data. Trend analysis, Hurst index, and correlation analysis were employed to investigate the spatiotemporal dynamics of vegetation CUE from 2000 to 2022 and the influence of hydrothermal factors on vegetation CUE. [Results] ① During 2000—2022, vegetation CUE increased significantly, with a growth rate of 0.012 per decade (p<0.05). The CUE values of key ecological functional areas in Inner Mongolia followed this order: Daxinganling and Xiaoxinganling Mountains > Hulun Buir > Hunshandake > Khorchin > Northern Yinshan. ② The spatial distribution of vegetation CUE in Inner Mongolia was higher in the west and lower in the east during the growing season, with an average annual value of 0.60. Among the key ecological functional areas, the highest vegetation CUE was observed in Hunshandake, while the lowest was in Khorchin. ③ Vegetation CUE exhibited an increasing trend in 83.53% of the study area, and this trend remained constant during the growing season. However, 72.14% of the study area would experience a decreasing trend in vegetation CUE in the future, with a higher proportion of key ecological functional areas showing a declining trend compared to those with an increasing trend. ④ Overall, vegetation CUE was negatively correlated with average temperature and positively correlated with cumulative precipitation and average soil moisture, with a stronger correlation observed with cumulative precipitation during the growing season. In contrast, vegetation CUE had a stronger correlation with average temperature than with cumulative precipitation and average soil moisture in Khorchin. [Conclusion] The carbon sequestration capacity of vegetation in Inner Mongolia increased significantly from 2000 to 2022 but would decline in the future. Precipitation was the main factor affecting changes in vegetation CUE in key ecological functional areas, while temperature was the dominant influencing factor in Khorchin.