In this paper, we study the morphologic interaction between graphene and Si nanowires on a SiO2 substrate, using molecular mechanics simulations. Two cases are considered: 1) a graphene nanoribbon intercalated by a single Si nanowire on a SiO2 substrate and 2) a blanket graphene flake intercalated by an array of Si nanowires evenly patterned in parallel on a SiO2 substrate. Various graphene morphologies emerge from the simulation results of these two cases, which are shown to depend on both geometric parameters (e.g., graphene nanoribbon width, nanowire diameter, and nanowire spacing) and material properties (e.g., graphene-nanowire and graphene-substrate bonding strength). While the quantitative results at the atomistic resolution in this study can be further used to determine the change of electronic properties of graphene under morphologic regulation, the qualitative understandings from this study can be extended to help exploring graphene morphology in other material systems. ; Comment: 23 pages, 7 figures