Limitations of traditional measurement methods have impeded progress in understanding the role of soil aggregation in protecting soil organic carbon (SOC) from decomposition by soil microbes living in pore spaces. In this paper, we used the Scanning Electronic Microscope (SEM) and X-ray micro Computed Tomography (micro-CT) to study the relationships of the aggregate pore structure and microbial distribution in the interior and exterior of soil aggregates, and thereby gained an insight into protection of carbon within macroaggregates of an undisturbed Mollisol in northeastern China. There were close relationships between soil pore structure and distribution of soil microbes and soil organic carbon (SOC), but they were different on the exterior and interior of soil aggregate. On the exterior of macroaggregates, there were negative relationships between soil porosities, the number of pores and SOC, especially for soil pores in the 10–30？μm and 30–100？μm classes, indicating these two pore sizes are unlikely to help sequester C. In contrast, there was a positive correlation between soil pores > 100？μm and SOC. Furthermore, soil pore structure had no impact on soil microbial biomass and density or on SOC contents in the interior of soil aggregates. This study provides a new method by combining SEM with micro-CT technology for linking soil structure and soil microbial properties with C sequestration and SOC changes.