This study investigated the distribution of aging depth gradients in styrene-butadiene-styrene modified bitumen (SBSMB) during natural aging. SBSMB was sourced from bitumen recycling tests and was stratified into upper, middle, and lower layers according to depth. To examine the effects of various aging depths, SBSMB samples from different depths were prepared for subsequent bitumen recycling tests. Then, studying the rheological performance of the SBSMB involved conducting multiple stress creep recovery tests. Subsequently, investigating the bee structure and nanoscale indicators of SBSMB at various aging depths involved utilizing atomic force microscopy testing. Finally, the Verhulst model was applied to assess the aging of SBSMB at different depths. The results have shown that natural aging has gradually diffused from the surface to the interior of the bitumen. An increase in aging time leads to a more pronounced aging effect at the upper levels and an accelerated the downward diffusion rate. This ultimately results in a gradient behavior of the rheological properties of SBSMB at different depths. The quantity of bee structures and the distribution density of bee structures in SBSMB both progressively decrease with increased aging depth. As aging time increases, the aging properties of SBSMB exhibit significant gradient behavior at different depths. Simultaneously, the Verhulst model accurately explain the aging trend of bitumen at different nanoscale depths.