Soil aggregates, which are the basic units of soil structure, play an important role in the carbon cycle of ecosystems. The pore characteristics of aggregates influence soil organic carbon sequestration. However, studies on SOC mechanisms in aggregates have been limited to Mollisols. This study was conducted as a long-term experiment established in 2004 with a corn-soybean rotation in Mollisols. There are three treatments, including rotary tillage without straw return (conventional tillage, CT), subsoiling without straw return (reduced tillage, RT), and no tillage with straw return (NT). The soil pore size distribution, shape parameters, extracellular enzymes activity, and carbon mineralization were measured. The results showed that 15-year no tillage and reduced tillage increased the total porosity and proportion of larger pores, but significantly decreased the proportion of smaller pores in situ soil columns. Conventional tillage exhibited the most complex pores because of the highest pore fractal dimension (2.75–2.90), anisotropy (0.366–0.516), and the lowest sphericity (5.1–28.7). As for the soil columns filled with > 2 mm aggregates, reduced tillage significantly increased the pore connectivity by 3.02–3.62 %, whereas no tillage had no effect. The structural equation modelling indicated that in soil columns filled with > 2 mm aggregates, pore shape parameters, particularly connectivity and anisotropy, positively influenced the activities of β-glucosidase and β-xylosidase directly, and positively affected soil carbon mineralization by influencing extracellular enzymes activity indirectly. The findings emphasize the importance of pore shape parameters effect on soil carbon sequestration, and will be helpful in comprehending the microscopic mechanisms of soil carbon sequestration in > 2 mm aggregates.