As we all know, karst areas have fragile ecosystems with strongly spatial heterogeneity and large carbon sink potential, which is sensitive to climate change. The change of land use pattern caused by karst ecological governance will lead to significant changes in ecosystem carbon storage, which has far-reaching impacts on the carbon cycle of the terrestrial ecosystem and regional ecological security. Take the Nanbei Panjiang River Basin in the typical karst area as an example, the InVEST model and hotspot analysis were used to assess the impacts of land use change on the spatial and temporal distribution of carbon stocks in the Nanbei Panjiang River Basin from 2000 to 2020. At the same time, the FLUS-Markov model was used to predict the changes of ecosystem carbon storages under different land use patterns, according to the characteristics of carbon storage agglomeration. Research results showed that: (1) from 2000 to 2020, the land use type in the study area has changed from high carbon density to low carbon density, resulting in a cumulative loss of 90.36×105 t in ecosystem carbon storage. (2) Carbon storage presented a spatial pattern of "low in west and high in east" area. Hot spots were concentrated in the east and southeast study area, while cold spots were mainly distributed in the west and southwest and weak significant areas were mostly in the north area. (3) Under different patterns, the carbon fixation capacities of each hot spots were significantly different. The average carbon density of hot spots was more than 155.40 t/hm2, which was obviously higher than the average carbon density of Nanbei Panjiang River Basin (143.59 t/hm2) in 2020. At the same time, the carbon sink capacity of the weakly significant area was close to the average level of the study area, and the carbon storage loss was less under Natural Development Pattern (NDP) and Economic Development Pattern (ECP). On the one hand, the carbon storage loss was severe in cold spot area under NDP and ECP, on the other hand the carbon sink increase rate was 1.38×105 t/a under Ecological Protection Pattern (EPP), which was significantly higher than the weakly significant area (0.30×105 t/a). In general, it means that the carbon fixation capacity of land use pattern under the influence of EPP is better than that of NDP and ECP. This study can provide some scientific basis for the optimization of land use pattern and ecosystem management in karst areas.