Understanding the mechanism of soil organic carbon (SOC) sequestration is of paramount importance in sustaining crop productivity and mitigating climate change. Long-term trials were employed to investigate the responses of total SOC and its pools, i.e., mineral-associated OC (MOC), particulate OC (POC, containing Light-POC and Heavy-POC), to fertilization regimes at Yangling (25-year), Tianshui (35-year) and Pingliang (37-year) under a rain-fed cropping system in the Loess Plateau. The fertilization regimes in each trial included three treatments, i.e., control (no nutrient input, CK), chemical fertilizers (CF), and organic manure plus chemical fertilizers (MCF). Relative to the CK, long-term fertilization appreciably increased SOC storage by 134, 89 and 129 kg ha⁻¹ yr⁻¹ under CF, and 418, 153 and 384 kg ha⁻¹ yr⁻¹ under MCF in plough layer soils (0–20 cm), respectively, at the Yangling, Tianshui and Pingliang sites. The MOC pools accounted for 72, 67 and 64% of the total SOC at the above three sites with sequestration rates of 76, 57 and 83 kg ha⁻¹ yr⁻¹ under CF and 238, 118 and 156 kg ha⁻¹ yr⁻¹ under MCF, respectively. Moreover, the MOC pool displayed a saturation behavior under MCF conditions. The POC accordingly constituted 27, 33 and 36% of SOC, of which Light-POC accounted for 11, 17 and 22% and Heavy-POC for 17, 16 and 15% of SOC, respectively. The sequestration rates of POC were 58, 32 and 46 kg ha⁻¹ yr⁻¹ under CF, and 181, 90 and 228 kg ha⁻¹ yr⁻¹ under MCF at the three respective sites, in which Light-POC explained 59, 81 and 72% of POC under CF, and 60, 40 and 69% of POC under MCF, with Heavy-POC accounting for the balance. Compared with CK, the application of CF alone did not affect the proportions of MOC or total POC to SOC, whereas MCF application markedly reduced the proportion of MOC and increased the POC ratio, mainly in the Light-POC pool. The distribution of SOC among different pools was closely related to the distribution and stability of aggregates. The present study confirmed that organic manure amendment not only sequestered more SOC but also significantly altered the composition of SOC, thus improving SOC quality, which is possibly related to the SOC saturation level.