Currently, few studies explore the internal phases of styrene-butadiene-styrene (SBS) modified bitumen at the nanoscale, though the surface phases of SBS modified bitumen have been deeply understood through a lot of research. The present study uses the atomic force microscopy (AFM) peak force quantitative nanomechanical mode (PF-QNM) to investigate the nanomechanical properties of the interior of linear SBS modified bitumen and corresponding mastics at the nanoscale. Firstly, the suitable experimental methods for the interior of bitumen and mastics are explored. Then, the phase relationship between surfaces and interiors of linear SBS modified bitumen is determined by analyzing nanomechanical properties. On this basis, in comparison with the internal phases of base bitumen, the effect of modifiers on phases is deeply investigated. Finally, the internal phases of linear SBS modified bituminous mastics are further investigated. The results reveal that the interior of linear SBS modified bitumen only has two phases, which form in a manner like periphase and paraphase on the surface. In contrast to base bitumen, linear SBS modified bitumen does not create new phases and change the properties of original phases in the interior, but affects the proportion of A-phase and B-phase and presents the homogenization. Furthermore, due to the influence of preparation methods, only the bitumen area away from the fillers can be imaged by AFM PF-QNM. It can be found that the addition of mineral fillers also slightly changes the internal phase distribution of linear SBS modified bitumen, while the effect is less than that of fillers on base bitumen.