To understand the influencing factors of soil organic carbon (SOC) storage in farmland and desert ecosystems in Xinjiang, the SOC storage data of 0-100 cm soil layer in Comprehensive observation field, Auxiliary observation field, and Household survey field from 2005 to 2020 were selected from the oasis farmland ecosystem in a warm temperate arid areas (Aksu), and the oasis farmland and desert ecosystem in a warm temperate desert area (Cele), and a temperate desert area (Fukang) in Xinjiang Uygur Autonomous Region. The results demonstrated that the average SOC storage in 0-100 cm soil layer from 2005 to 2020 was Aksu (5.17 kg/m²)>Fukang (4.20 kg/m²)>Cele (2.96 kg/m²). The SOC in 0-20 cm, 20-40 cm, and 40-60 cm soil layers accounted for 27.3%-35.3%, 23.1%-24.6%, and 15.8%-17.5% of 0-100 cm soil layer reserves, respectively. The SOC storage was the highest in the Auxiliary observation field with the highest fertilizer application and the lowest irrigation at Aksu. The fertilization and irrigation measures of the Household survey field and Auxiliary observation field were the most beneficial to increase SOC storage at Cele and Fukang, respectively. In general, the soil water content and the aboveground biomass were positively correlated with the SOC storage in the 0-100 cm soil profile. The annual mean temperature was negatively correlated with the SOC storage in the 0-40 cm soil layer. There was no correlation between annual mean temperature and the SOC storage when different ecological stations were considered separately. The aboveground biomass was positively correlated with the SOC storage at Cele and Fukang, but was negatively correlated with the SOC storage in the 0-40 cm soil layer at Aksu. The amount of pure potassium applied was positively correlated with the SOC storage in the 0-60 cm soil layer at Cele, but was negatively correlated with the SOC storage in the 40-100 cm soil layer at Fukang. In conclusion, farmland management measures of irrigation and fertilization are beneficial to increase SOC storage in arid areas, when compared with natural deserts and farmland without fertilization. Reasonable agricultural management should be developed in different ecological stations according to their regional characteristics to improve SOC storage.