[Objective] This paper is oriented to explore effects of increased or decreased application of organic manure on stability and cement (e.g. organic carbon and iron-aluminium oxides) of soil aggregates stability in red paddy soil of a long-term field fertilization experiment.[Method] In the 35-year-old long term field experiment, on the premise of guaranteeing normal development of the original stationary experiment, the treatments, which used to be applied with chemical fertilizer, changed to be applied with organic manure instead and the treatments, which used to be applied with original manure, changed to be applied with chemical fertilizer or remained to be applied with organic manure, but at a higher rate. Soil samples were collected from the tillage soil layers of the treatments and analyzed for changes in fractionation, stability, contents of total organic carbon (TOC) and its fractions, and content of iron-aluminium oxides of soil aggregates. Based on the analysis of the relationship between aggregates stability and cement, mechanism of their interactions was explored with correlation analysis and path analysis methods.[Result] Results show that there was no obvious changes in average weight diameter (MWD) of the soil aggregates after application of organic manure at a higher rate in Treatment CF (application of chemical fertilizer) and Treatment NOM (application of organic manure at a normal rate), but there were in content of oxidizable organic carbon (EOC), which increased by 87.44% and 20.53%, respectively, in the organic carbon fraction, and in content of fine particulate organic carbon (fPOC), which increased by 26.94%, in Treatment N-H (treatments changed from normal to high in organic manure application rate); MWD decreased significantly or by 8.39% and 6.80%, respectively, in Treatment H-C (treatment changed from application of organic manure at a high rate to application of chemical fertilizer) and treatment N-C(treatments changed from application of organic manure at a normal rate to application of chemical fertilizer); TOC, coarse particulate organic carbon (cPOC) and light organic carbon(LFOC) decreased by 23.48%, 30.09% and 25.29%, respectively, in treatment H-C (treatment changed from application of organic manure at a high rate to application of chemical fertilizer), but TOC and its fraction did not vary much in Treatment N-C (treatment changed from application of organic manure application of chemical fertilizer treatment); and no matter whether in treatments with application of organic manure increased or decreased in rate, the content of Fe-Al oxides varied irregularly. Correlation analysis and analysis using the structural equation model (SEM) show that the content of >0.25 mm aggregates increased along with growing organic carbon fraction and with rising free iron oxide (Fe_d) content, but decreased with rising chelated oxide (Fe_s) content, and >0.25 mm aggregates were the only factor directly affecting MWD; changes in organic manure application rate induced the content of light organic carbon (LFOC) and EOC raised or declined in red paddy soils, resulted in the synergistic variation of Fe_d and Fe_s, which eventually led to changes in content of >0.25 mm aggregates. In terms of effect coefficients of the factors affecting MWD and >0.25 mm aggregates, an order of EOC > LFOC > Fe_d> Fe_s,was observed and organic carbon and its fractions were the principal affecting factors in the red paddy soil.[Conclusion] The fraction of >0.25 mm aggregates in the red paddy soil plays a key role in aggregate stability, and the fraction of active organic carbon is the major factor affecting formation and destruction of large-sized soil aggregates.