Considering the increased application of high reclaimed asphalt pavement (high RAP) content mixtures, the biorejuvenator attracts increasing attention during the pavement maintenance and rehabilitation process, because this method can be implemented with ease and high effectiveness. However, the aging mechanism of biorejuvenated asphalt at a microscale is not well-understood. The microscale analysis provides a way to acknowledge how the biorejuvenator works. Therefore, this study aims to characterize the physical-structural and chemical changes of biorejuvenated asphalts of different aging levels at a microscale. The methodologies adopted include component analysis, atomic force microscopy (AFM), and Fourier-transform infrared spectroscopy (FTIR). In AFM tests, roughness and percentage of bee structures were compared in quantifying the surface morphology changes during aging. Correlation analysis was conducted between the microstructure and component analysis. Young’s modulus and adhesive forces were measured to quantify the micromechanical properties. FTIR spectra were used to investigate the aging mechanism. Results revealed that saturates, aromatics, resins and asphaltenes (SARA) fractions of original asphalts and biorejuvenated asphalts changed in the same way during aging. More special variations were found in aged biorejuvenated asphalt, and saturates content was discovered to determine the variation of bee structures’ percentage. The adhesion forces changed in different ways because of the different original asphalts, and the modulus index demonstrated that biorejuvenated asphalt aged faster than the original asphalt. The FTIR test demonstrated the new aldehyde in the biorejuvenator may be the reason for the accelerated aging of biorejuvenated asphalt.