To elucidate the spatiotemporal evolution of soil organic carbon (SOC) in irrigation desert soil under long-term fertilization, this study utilized a long-term field experiment established in 1982 in Zhangye, Gansu Province. The regulatory effects of eight fertilization treatments (CK: no fertilization; N: nitrogen; NP: nitrogen + phosphorus; NPK: nitrogen + phosphorus + potassium; M: manure; MN: manure + nitrogen; MNP: manure + nitrogen + phosphorus; MNPK: manure + nitrogen + phosphorus + potassium) on SOC content and storage across the 0-200 cm soil profiles under three cropping systems (wheat-wheat-maize rotation, wheat/maize intercropping, and maize monoculture) were systematically analyzed during two sampling periods (2003: after 22 years; 2022: after 41 years). The results showed that: 1) Fertilization regimes significantly influenced SOC accumulation efficiency, with SOC content ranked as MNP, MNPK>M, MN>N, CK>NP, NPK. SOC in CK and N declined continuously, while M markedly enhanced SOC, with MNPK showing the greatest increase. 2) SOC exhibited distinct vertical stratification, with topsoil (0-20 cm) showing the highest SOC content and storage (2003: 9.67-16.15 g/kg, 28.7-45.5 t/hm²; 2022: 10.47-15.70 g/kg, 29.5-44.3 t/hm²), decreasing exponentially with depth. 3)Cropping systems modulated carbon use efficiency. Organic manure application achieved a carbon sequestration rate of 38.6% with 132.2 kg organic carbon consumed per ton of grain yield under wheat rotation, whereas the carbon sequestration rate decreased to 24.7% and the carbon consumption increased to 156.6 kg/t under maize intercropping/monoculture, highlighting the role of crop configuration in balancing carbon input and sequestration. In conclusion, organic-inorganic combined fertilization synergistically enhances topsoil carbon capacity and subsoil carbon stability, serving as a core strategy for optimizing carbon sequestration and grain productivity in arid irrigation-silted soils. In addition, it is recommended to implement a wheat maize rotation system in irrigated desert soil areas to enhance soil carbon sequestration function. These findings provide critical scientific insights for designing regional agricultural carbon neutrality pathways.