Understanding the microstructure evolution during the cyclic freezing-thawing process is crucial to studying the deterioration mechanisms of concrete under cyclic freezing-thawing. In this study, air voids were entrained into cement mortar and paste by AEA and polymeric microspheres. Mercury intrusion porosimetry (MIP) and micro-CT techniques were integrated to investigate the microstructure of the specimens with various freezing-thawing cycles. After subjecting the Ref. and AEA mixed mortar to 100 and 200 freezing-thaw cycles, an increase in porosity and pore entrapment was observed from the MIP results, suggesting the occurrence of damage induced by cyclic freezing-thawing. Conversely, in the microspheres mixed mortar, the presence of surface adsorbed moisture led to an initial increase in porosity and pore entrapment after 100 freezing-thaw cycles, followed by a decrease after 200 cycles, indicating a healing effect. Micro-CT analysis revealed that while the AEA mixed specimens exhibited higher air content than the microspheres mixed specimens, the latter showed a greater number of voids, which ultimately enhanced their resistance to freezing-thawing. The micro-CT results unveiled that air bubbles tended to merge in AEA mixed specimens, adversely affecting their resistance to freezing-thawing. Conversely, the microsphere-incorporated specimens displayed smooth void distribution curves, indicating a well-distributed air void system that enhances their freezing-thawing resistance. This work suggests that microspheres can be a great candidate for air-entraining materials. Combining the MIP and micro-CT analysis can better understand the microstructure change of concrete with cyclic freezing-thawing.