Abstract: Carbon stocks play a pivotal role in maintaining ecosystem balance. Due to its unique natural endowment, the highland alpine climate zone has rich carbon stocks, and the estimation and analysis of its carbon stocks are of great reference value for coordinating and optimizing the regional land-use pattern and improving the potential of regional ecosystems in terms of carbon stocks. Taking the three Prefectures, the typical plateau alpine climate zone, in Sichuan Province as an example, the land use changes from 2000 to 2020 was understood, the spatial and temporal changes of its carbon stock was estimated, and the spatial autocorrelation of its district and county carbon stocks was analyzed. The results were as follows: (1) From 2000 to 2020, grassland and woodland accounted for the largest proportion in the study area, accounting for more than 90% of the total area of the three Prefectures in Sichuan Province. From 2000 to 2020, the land use transfer area accounted for 5.28% of the total area, and wetlands had the highest conversion probability. (2) The carbon stocks in 2000, 2010 and 2020 were 3116.24×10⁶, 3115.31×10⁶ and 3112.68×10⁶, respectively, showing a continuous decreasing trend. During the studied 20-year period, the carbon storage in 24 districts and counties was increased, while in the other 24 districts and counties the carbon storage was decreased, indicating that change in carbon stocks in the study area was in a differentiated state in terms of districts and counties. (3) The global autocorrelation results showed that there was a positive correlation in terms of districts and counties for the carbon storage. The local autocorrelation results showed that the high-high accumulation area of carbon stocks was in the west part of the study area, and the low-low accumulation area was in the south part of the study area. This study contributes to an in-depth understanding of carbon stocks in the three prefectures of Sichuan and assists in the construction of ecological civilization and achieving the goal of "double carbon".