Because of their attractive chemical and physical properties, graphitic nanomaterials and their derivatives have gained tremendous interest for applications in electronics, materials, and biomedical areas. However, few detailed studies have been performed to evaluate the potential cytotoxicity of these nanomaterials on living systems at the molecular level. In the present study, our group exploited the isobaric tagged relative and absolute quantification (iTRAQ)–coupled two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) approach with the purpose of characterizing the cellular functions in response to these nanomaterials at the proteome level. Specifically, the human hepatoma HepG2 cells were selected as the in vitro model to study the potential cytotoxicity of oxidized single-walled carbon nanotubes (SWCNTs) and graphene oxide (GO) on the vital organ of liver. Overall, 30 differentially expressed proteins involved in metabolic pathway, redox regulation, cytoskeleton formation, and cell growth were identified. Based on the protein profile, we found oxidized SWCNTs induced oxidative stress and interfered with intracellular metabolic routes, protein synthesis, and cytoskeletal systems. Further functional assays confirmed that oxidized SWCNTs triggered elevated level of reactive oxygen species (ROS), perturbed the cell cycle, and resulted in a significant increase in the proportion of apoptotic cells. However, only moderate variation of protein levels for the cells treated with GO was observed and functional assays further confirmed that GO was less cytotoxic in comparison to oxidized SWCNTs. These finding suggested that GO was more biocompatible and could be a promising candidate for bio-related applications.