It is an inevitable requirement of environmentally sustainable development to bring ecological resources into the overall management of the economic system. For ecologically fragile areas, it is particularly important to strengthen resource management under changing environmental pressures. This paper attempts to understand the change characteristics of carbon fixation function of ecosystem from the perspective of system structure, and carries out spatial analysis of carbon fixation function in Yulin area combined with landscape structure index. From 2000 to 2020, the carbon sequestration service value of Yulin’s ecosystem continued to increase, and the growth rate was fast in 2000～2010 and slowed down in 2010～2020. In terms of spatial distribution, the carbon sequestration value per unit area s decreases from southeast to northwest, and the growth rate in southeast is also faster. Industrial activities are the main factor to form the northwest and southeast division of carbon sequestration value of Yulin, and the southeast counties are more affected by the change of ecosystem structure. The results of the study suggest that we should comprehensively consider the structure of the ecosystem to improve the potential functionality of the regional ecosystem when implementing ecological construction and restoration projects in the ecological fragile areas in the future.