Soil is an important resource for human survival. Soil aggregate, as the basic unit of soil structure, can not only improve soil fertility, regulate the bioavailability of nutrients, nut also, but nutrients also enhance soil anti-erosion ability. In this research, four fertilization patterns were applied in a rice-wheat rotation system at Shanghai Zhuanghang long-term positioning test station for six years, which were non-fertilization (CK), conventional inorganic fertilization (CF), straw returning to field with slow release fertilizer (SRF), and mixed organic fertilizer with chemical fertilizer treatment (OCF). It provides a theoretical basis for revealing the influence mechanism of fertilization methods on the formation and evolution of soil fertility. SRF and OCF increased the SOC contents in 0-20 cm and 20-40 cm soil by 10.06%, 19.23% and 9.84%, 16.79%, respectively. OCF also increased the level of C/N in 0-20 cm (16.44%). There was no significant difference in TN contents in both 0-20 cm and 20-40 cm soil layers under CF, SRF, and OCF. But they were all higher than that of CK. Compared with CK, SRF significantly improved R_0.25 in 0-20 cm soil layer by 10.93%. OCF increased the R_0.25 in 20-40 cm, compared with the other three treatments (32.62% CK, 19.75% CF, 19.44% SRF) (p<0.05). Compared with CF, SRF and OCF increased MWD (1.54%~16.92%, 2.17%~28.26%) and GMD (5.88%~14.71%, 13.04%~39.13%), decreased D (1.11%~2.09%,4.99%~5.44%) in the 0-20 cm and 20-40 cm soil layers, with the more prominent effect for OCF (p<0.05). In conclusion, both SRF and OCF were beneficial to soil fertility improvement, and effect of OCF was more significant. The correlations between MWD and GMD and soil SOC and TN were significant, which, therefore, were suitable for revealing the relationships between aggregation and the soil nutrient contents. However, there was no significant correlation between soil nutrients and D.