Carbonaceous nanoparticles (CNPs), including carbon black, carbon nanotubes, and graphene nanopiece, were selected as nanoadditives for investigating the rheological behavior dependence of their polymer-based composites on morphological and interfacial structure. Polypropylene (PP) was adopted as matrix and a series of contents of CNPs were used for sample compounding. With identical concentration, the morphological structure of CNPs was emphasized as the dominant effect affecting the shear viscosity and the compressibility of PP/CNPs melts. The viscosity dependence on the CNPs contents and physical structure, such as particle size, aspect ratio, and specific area, was fully discussed in this work. The newly-introduced inner voids, induced around the interface region between matrix and CNPs during physical mixing, were contributive to the rheological deviation, which was further reflected from the melt compressibility.