The characteristics of aerobic granules for wastewater treatment are greatly related to their complex internal structure. However, due to the limitation of characterizing methods, information about the granule internal morphology and structure is very sparse, and mechanism of mass transfer process is yet unclear. In this work, the internal structure of aerobic granules was explored using nitrogen adsorption method and confocal laser scanning microscopy technique. It was found that aerobic granules had multiporous structure with cross-linked gel matrix structure. With a consideration of the hydrodynamic regime and the porous structure of granules, a two-dimensional percolation model was established to describe the mass transfer in granules. With the approaches, interesting and useful results regarding the pore distribution and mass transfer in aerobic granules have been obtained. The results demonstrate that the intragranule convection could enhance mass transfer, hence ensure an efficient and stable operation of aerobic-granule-based reactors. Such approaches might also be applicable to characterizing the multiporous structure and mass transfer of other microbial aggregates for wastewater treatment.