Physical protection of carbon (C) in soil aggregates is an important mechanism affecting soil organic carbon (SOC) stocks but there is little information on the turnover dynamics of aggregates in dryland red soils after different long-term fertilizer application practices. Different aggregate size classes in zero fertilizer (CK), chemical fertilizer (CF) and chemical fertilizer combined with manure (MCF) treatments were examined. The RothC model was used to simulate C inputs based on SOC dynamics, the carbon, aggregation and structure turnover (CAST) model was used to evaluate soil structure and C sequestration at different aggregate size classes with time. MCF treatment significantly (p < .05) increased total macroaggregate C, and fractions of macroaggregate C compared with the other two treatments because C inputs and C sequestration rate increased significantly (p < .05) according to RothC model simulation. The CAST model performed well in simulating the changes in soil structure and organic C stocks in different aggregate size classes with time. The simulation results indicate that particulate organic matter (POM) is the primary source of aggregate turnover, that free silt-clay particles have a more rapid turnover than the silt-clay particles in other (larger) aggregates, and that the disruption criterion for aggregate distribution in CAST model parameters followed the sequence MCF > CF > CK in the low pH and low SOC red soil. Overall, the CAST model is a good tool for simulation of aggregate dynamics in red soil under different fertilizer application treatments.