The induction of autophagy by nanoparticles causes nanotoxicity, but appropriate modulation of autophagy by nanoparticles may have therapeutic potential. Multiwalled carbon nanotubes (MWCNTs) interact with cell membranes and membrane-associated molecules before and after internalization. These interactions alter cellular signaling and impact major cell functions such as cell cycle, apoptosis, and autophagy. In this work, we demonstrated that MWCNT-cell interactions can be modulated by varying densely distributed surface ligands on MWCNTs. Using a fluorescent autophagy-reporting cell line, we evaluated the autophagy induction capability of 81 surface-modified MWCNTs. We identified strong and moderate autophagy-inducing MWCNTs as well as those that did not induce autophagy. Variation of the surface ligand structure of strong autophagy nanoinducers led to the induction of different autophagy-activating signaling pathways, presumably through their different interactions with cell surface receptors.