Terrestrial ecosystem carbon storage is of great significance for predicting climate change, greenhouse gas emissions and reductions. Land use pattern change is the basis for studying terrestrial ecosystem carbon storage, which directly affects the structure and distribution of terrestrial ecosystems, as well as changes terrestrial ecosystem carbon reserves. Taking the upper Fenhe River as an example, this paper analyzed the land use change from 2007 to 2017, and the SD_CLUE-S composite model was used to simulate the land use pattern under natural growth and ecological protection environment. Based on the land use data, the InVEST model was used to measure the carbon storage of ecosystem in 2007 to 2017 and in the future under different scenarios. The results showed that the area of grass land, unused land and water body in the upper reaches of Fenhe River decreased from 2007 to 2017, while the cultivated land, construction land and forest land increased. The land use pattern in 2030 under natural growth scenarios and ecological protection scenarios was quite different. The cultivated land, construction land, forest land and water body indicated an opposite trend. In 2017, the carbon storage and carbon density of the upper Fenhe ecosystem were 58997910.98 t and 147.54 t/hm², which increased by 1237143.02 t and 3.09 t/hm² compared with 2007. Under the natural growth scenario from 2017 to 2030, the carbon storage and carbon density of the ecosystem in the upper reaches of Fenhe decreased significantly, mainly due to the decrease in forest land and grass land, the increase in construction land, and the significant increase under the ecological protection scenario. The carbon storage and carbon density were 59142210.16 t and 147.95 t/hm², respectively. Ecological protection scenarios can effectively improve the regional ecosystem carbon storage, but at the same time, sustainable social and economic development must be considered. Therefore, in the future development plan, the research area should coordinate various resources based on ecological protection scenarios to ensure economic development.