It is demonstrated using molecular dynamics (MD) simulations that P-doped silicon nanowires (Si NWs) can activate graphenes self-scrolling onto Si NWs and thus produce new kinds of graphene nanoscroll (NS)/Si core/shell heterojunctions. The simulations show that graphene sheets can fully self-scroll onto Si NWs when the Si NW radius is larger than a threshold of about 5 Å, forming a stable core/shell structure. It is the van der Waals force that plays a primary role in the self-scrolling process. The configuration of the graphene–Si heterojunction depends significantly on the diameter of the Si NWs. The final NS becomes multiwalled with increasing graphene length when the diameter of the Si NWs is larger than a threshold of about 6 Å. The zigzag NS is proved to be the most stable, while the chiral NSs are unstable and tend to evolve into zigzag NS and a model is set up to interpret the tendency from the standpoint of bond. It is demonstrated that the graphene width has no influence on the self-scrolling process at all. Compared with the conventional fabricating method, the new self-assembling one occurs at room temperature and the thickness of the NSs can be controlled accurately. Besides, the unique structure of the graphene/Si core/shell heterojunctions will significantly enhance their applications in nanoelectronic devices, hydrogen storage, solar cells, chemical or biological sensors, and energy storage in supercapacitors or batteries.