As one of the prospective two-dimensional nanomaterials, black phosphorus (BP), which has excellent physical and chemical properties, has witnessed quick development in theranostic applications. The more recent advances in combining BP nanosheet (NS) with nanoparticles exhibit new opportunities to develop multifunctional nanocomposites. However, more effort should be devoted to elucidate the nanomaterial-cell interaction mechanism before the bio-applications of BP-nanoparticle hybrids. Herein, the intracellular behaviors of BP-gold nanoparticles (BP-Au NSs) are first investigated using the surface-enhanced Raman scattering (SERS) technique. The presence of Au nanoparticles on the surface of a BP sheet allows nanohybrids with excellent SERS activity to enhance the intrinsic Raman signals of cellular components located around the NSs. Data from an endocytosis inhibitor blocking assay reveal that the nanohybrids are mainly taken up by macropinocytosis and caveolae-dependent endocytosis, which are energy-dependent processes. Associated with colocalization experiments, nanohybrids are found to internalize into lysosomes and the endoplasmic reticulum. Moreover, the SERS difference spectrum is extracted after Raman-fluorescence colocalization statistical analysis to distinguish the molecular structural differences in the biochemical components of the two organelles. These findings supply a definite cellular mechanistic understanding of the nano-biointeractions of nanocomposites in cancer cells, which may be of great importance to the biomedical applications of nanotechnology in the future.