In this study, a 3-year fixed-site field experiment was conducted to investigate the influence of different tillage practices and straw incorporation on soil aggregates, retention of organic carbon, and crop yields. Six treatments were set up: plough + chemical fertilizer (T1), plough + straw incorporation + chemical fertilizer (T2), rotary tillage + chemical fertilizer (T3), rotary tillage + straw incorporation + chemical fertilizer (T4), no-tillage + chemical fertilizer (T5), no-tillage + straw incorporation + chemical fertilizer (T6). The results showed that, compared to plough tillage, the macroaggregates (> 2mm, A1) in surface soil (0—20 cm) under no-tillage increased by 35.79%, the medium-aggregates (2~0.25 mm, A2) increased by 30.81%, and the microaggregates (0.25~0.106 mm, M1) increased by 25.80%. Soil aggregates of T6 had the highest capability to hold organic carbon, the contents of soil organic carbon in A1, A2 and M1 under T6 were 25.04%, 28.55% and 18.12% higher respectively than those under T1. The sub-surface soil (20—40 cm) showed the similar trend with surface soil. The difference was that the proportion of aggregated carbon retained in sub-surface soil layer was higher than that in surface soil. The crop residue was brought into deep soil by plough, which increased the accumulation of organic carbon in deeper soil. The results also showed that the increase of carbon in soil profile mainly came from the import of crop residue carbon. Deep plough was beneficial to raise the retention of organic carbon in deep soil profiles. In terms of crop yield, the equivalent rice yield under the conventional tillage was higher compared with the conservation tillage. The main reason should be that the conservation tillage not only hindered the growth of seedlings, but also reduced the effective panicle number for the mature rice and wheat.