The interaction between soil organic carbon (SOC) and clay minerals is a critical mechanism for retaining SOC and protecting soil fertility and long-term agricultural sustainability. The SOC composition and minerals speciation in clay fractions (<2 μm) within soil aggregates under straw removed (T) and straw incorporation (TS) conditions were analyzed by X-ray diffraction, Fourier transform infrared spectra and X-ray photoelectron spectroscopy. The TS treatment promoted enrichment of clay in aggregates. The TS increased the contents of SOC (27.0–86.6%), poorly crystalline Fe oxide (Fe_o), and activity of Fe oxides (Fe_o/Fe_d); whereas, it reduced the concentrations of free Fe oxide (Fe_d) in the clay fractions within aggregates. Straw incorporation promoted the accumulation of aromatic-C and carboxylic-C in the clay fraction within aggregates. The relative amount of hydroxy-interlayered vermiculite, aliphatic-C, and alcohol-C in the clay fractions within the macroaggregates was higher than that microaggregates, whereas the relative amounts of illite, kaolinite, Fe(III), and aromatic-C had a reverse tendency. The hydroxy-interlayered vermiculite in clay fractions showed positive correlation with the amounts of C–C(H) (r = 0.93) and C–O (r = 0.96 *, p < 0.05). The concentration of Feo and Feo/Fed ratio was positively correlated with the amounts of C=C and C(O)O content in clay within aggregates. Long-term straw incorporation induced transformation of clay minerals and Fe oxide, which was selectively stabilized straw-derived organic compounds in clay fractions within soil aggregates.