The aggregates are essential components of soil, and the destruction of soil aggregates by cultural practice tends to expose the previously protected soil organic carbon (SOC) to decomposition. Yet, the temperature response of SOC mineralization (Q10) in soil aggregates and the underlying microbial mechanisms remain unclear. We aimed to investigate the Q10 of SOC and maize straw mineralization and microbial enzyme activity in response to aggregate class sizes. By adopting isotopic analysis and a short-term microcosm experiment (with maize straw incorporation). We measured Cumulative CO2 emission, soil and straw-derived CO2, extracellular enzyme activities, and Q10 within bulk soil (BS) and isolated macro-aggregates (MAA) and micro-aggregates (MIA) under two temperature levels of 15 °C and 25 °C. Our results showed that MIA had a higher cumulative CO2 emission ranging from 208.0 to 1649.5 µg CO2-C g−1 soil at 25 °C compared to MAA 197.4 -1568.7 µg CO2-C g−1 soil and BS 171.2–1435.0 µg CO2-C g−1 soil. The same trend of CO2 emission between MAA, MIA, and BS was found at 15 °C, with lower CO2 emission, indicating a declined mean Q10 in MIA (1.8) followed by MAA (1.7) and BS (1.5). Both SOC and straw-derived CO2 efflux are larger in MIA compared to MAA and BS, e.g., the cumulative maize straw-derived CO2 efflux was 521.13, 640.92, and 698.29 µg CO2 -C g−1 soil for BS, MAA, and MIA, at 25 °C,. Higher CO2 and Q10 in smaller aggregates might be due to greater microbial pressures (qCO2) and higher activity of glucosidase activity rather than cellobiohydrolase. Overall, the findings showed that microbial mechanisms underlying soil CO2 emission feedback to enhanced temperature in relation with soil aggregates.