We insert carbon nanotubes (CNT) as nanospacers to modulate the microstructure of multilayer stacking graphene. Nanospacers can increase interlayer distance and reduce interlayer interaction. The graphene/CNT stacking structure is experimentally fabricated and Raman spectroscopy verifies the reduction in interlayer interaction within the stacking structure. Thus, we study the microstructure of the stacked graphene and CNTs by molecular dynamics simulation to systematically investigate the effect of CNT insertion. The distribution distance, size, and arrangement of the CNT can modulate the interlayer distance. The graphene/CNT stacking structure exhibits two stable configurations: the upper-layer suspension and interlayer adsorption.