Aging of the asphalt binder can affect the durability of the asphalt pavement during its lifetime. The purpose of this study is to evaluate the performance of asphalt binders based on microscopic data under various aging environments. In this study, a Performance Grade (PG) 64-22 binder (control), collected from two different crude sources along with their modified counterparts were evaluated. For microscopic evaluation, an Atomic Force Microscopy (AFM) tool was used to measure the aging effects on the binders’ rheological and mechanical properties at the molecular level. Additionally, the Rotational Viscosity (RV) and Dynamic Shear Rheometer (DSR) tests were performed on the asphalt binder samples. All binder samples were tested under three different aging conditions namely, unaged, short-term aged, and long-term aged. The AFM test results showed that the microstructures presented on binder’s surface were largely affected (e.g., dispersed and/or reformed) because of the aging, resulting in variations of mechanical properties (e.g., modulus, adhesion, deformation, etc.). The modulus and adhesion values were found to increase, whereas deformation was decreased due to aging. The DSR test results showed that the complex (dynamic) modulus increased for all binders irrespective of the extent of aging and binder’s crude sources. Such observations agree with the AFM test results. The findings of this study will help the asphalt industries and pertinent transportation agencies to gain micro-level knowledge into the aging effect on the properties of the asphalt binders.