Both iron (Fe) oxide and soil organic carbon (SOC) content, among other factors, drive the development and subsequent stability of soil aggregates. However, the mechanism of these drivers in paddy-upland rotation systems with straw residue incorporation is not well understood. In this multiyear (2011-2017) trial, we sought to study the factors which drive the stability of soil aggregates in such a rice-rape (RR) agronomic system. In order to examine the effect of straw residue incorporation and potassium fertilization on soil aggregation dynamics, we divided our trial into four treatments: inorganic phosphorus (P) and nitrogen (N) fertilizer; inorganic NPK fertilizer; inorganic NP fertilizer plus straw residue; and inorganic NPK fertilizer plus straw residue. Treatments which incorporated straw residue significantly increased both the geometric mean diameter (GMD) and the mean weight diameter (MWD) of soil aggregates. Soil aggregate stability was greater after rape harvest than after rice harvest, while SOC shows the opposite trend. Straw residue incorporation increased the SOC and, specifically, concentrations of aliphatic-C and aromatic-C, particularly in aggregates greater than 0.25 mm. Straw residue addition significantly increased both the amorphous (Feo) and complex iron oxide (Fep) contents of soil. In both bulk soil and in aggregates greater than 5 mm, SOC and Fep were positively correlated with MWD, while in aggregates less than 5 mm, Feo was positively correlated with MWD. Overall, we suggest that the increased concentrations of SOC, alkane-C, Feo, and Fep in soils after incorporation of straw residue were responsible for increasing soil aggregate stability.