The potential of Raman spectroscopy in anticancer drug study has been demonstrated, yet its ability to character systematic cellular changes caused by multi-component drugs has not been explored. Here we used micro-Raman spectroscopy combined with bright field imaging to study Compound Kushen injection (CKI) at a sub-cellular level including intracellular vesicles(IVs). In our report, CKI caused dysfunction of DNA replication and repair was displayed by Raman spectrum (RS) from the cell nucleus. Meanwhile, the dynamics of CKI induced intracellular vesicles and cell component deconstruction was delineated by RS from the cytoplasm and IVs. The lipids-related biomolecular changes were also presented by the cytoplasm RS: the lipids level in the cytoplasm first descended then uprising. In conclusion, this study validated the mechanism and displayed the dynamics of CKI in treating cancer cells. We proved the capability of subcellular micro-Raman spectroscopy for detecting systematic cellular changes and its application for multi-component drug evaluation.