Abstract: In this study the effects of tillage methods (flooded paddy field, FPF; conventional paddy-upland rotation tillage, CR; combing ridge with no-tillage, RNT) on soil aggregates as well as on the soil organic matter (SOM) fractions protected by soil aggregates were investigated in a long-term experimental site established in 1990, Chongqing City, China. The results showed that compared with FPF and CR, RNT reduced the disruption of macro-aggregates. In 0–10 cm layer, the content of macro-aggregates in RNT was 1.48 and 1.32 times greater than that in FPF and CR, respectively, while the content of micro-aggregates decreased in RNT, and there was a similar trend in >10–20 cm layer. Under these three tillage methods, the distribution pattern of soil organic carbon (SOC) and soil organic nitrogen (SON) in aggregates were similar, and both of them had an enrichment trend to macro-aggregates, but concentration of SOC and SON was significantly higher under RNT than that in FPF and CR. The results of particulate organic matter (POM) showed that the amount of light fraction (LF) had no significant difference between RNT (1.92 g/kg) and CR (1.70 g/kg), but they were both higher than that in FPF (1.42 g/kg). Total intro-particulate organic matter (iPOM) concentration in FPF, CR, and RNT was 0.96, 1.12, and 2.14 g/kg, respectively. The level of fine iPOM in RNT was 3.06 and 2.46 times greater than that in FPF and CR, which accounted for 57% of the difference in total POM between RNT and FPF (66%, CR). The amount of coarse iPOM was only 1.56 and 1.40 times greater than that in FPF and CR, which accounted for only 18% and 19% of the difference in total POM. Though there was a similar trend in >10–20 cm layer, the difference of coarse iPOM held more share of the difference in total POM than that in 0–10 cm layer. In conclusion, RNT reduced macro-aggregates breakdown, and improved the formation of aggregates from micro-aggregates, which decreased the turnover rate of soil aggregates, favored the sequestration of fine iPOM and promoted the purple paddy soil ability to fix and accumulate carbon.