[Objective] The pore structure and spatial distribution of intra-aggregates in soils determine many functions of soil aggregates and physical, chemical, and biological processes occurring in aggregate. The objectives of this study were (i) to examine the three dimension (3D) pore characteristics of intra-aggregate pores; (ii) describe the spatial distribution of macropores (>30 ?m) within aggregates, and (iii) to analyze the relation between pore structure and functions of the aggregates. [Method] The 3-5 ?m aggregate of two red soils (named as Q4 and Q12) with different stability were used in this study. Synchrotron radiation X-ray microcomputed tomography (SR-mCT) was used to scan the 3-5 mm aggregate of two red soils. A combination of SR-mCT and image analysis was applied to describe the intra-aggregate pore characteristics and pore spatial distribution within the aggregates. [Result] The SR-mCT images of aggregates indicated a considerable difference in the morphology, pore size, and pore growth direction of intra-aggregate in two soil samples. The soil Q4 was characterized by abundance macropores, multifarious pore growth direction and pore size distribution, whereas soil Q12 by dense micropores, and consistent pore grow direction. They have similar single pore shape, while different interconnected pore shape. The porosities of 5-30, 50-80, and >80 ?m in soil Q4 were significantly higher than those of soil Q12. The abundance of macropores (>30 ?m) within soil Q4 aggregates was relatively larger in the center part of aggregate, while soil Q12 had a uniform spatial pattern with larger in the outer part of aggregate. [Conclusion] The SR-mCT system could clearly describe pore diversity and spatial variation of intra-aggregates without disrupting the aggregate microstructure, which could be effectively to predict the function and physical processes of the aggregates.