Molecular profiling and accurate damage analysis of complex biomolecular events in tumor cells are critical to the diagnosis and treatment of cancer.However, due to sensitivity limitation and dynamic and complex nature of apoptosis process, label-free detection of cellular DNA damage during cancer therapeutic treatment, at the DNA bases level, is still a huge challenge. Herein, by designed preparation of novel and uniform plasmonic sunflower-like assembly gold (Au) nanostructure that capable of efficient DNA capture and providing high-density “hot spots” for SERS enhancement, we succeeded in sensitive and reliable SERS detection of DNA damage in apoptotic cancer cells at the DNA bases level. The chemical structure damage of cellular DNA caused by electrostimulus-induced cell apoptosis was revealed and discriminated at the bases level, for the first time, by label-free SERS detection with the nano-sunflowers. The SERS results showed that the external electrostimulus (at 1.2 V, for 5 min) was almost harmless to normal healthy cells but it caused pronounced double strands break and Adenine (A) base damage in cancer cell DNAs, which effectively destroyed the reproduction and transcribe of DNA to harass cancer cell mitosis and ultimately induce cell apoptosis. The finding provides deep insights into molecular genomic DNA damages of cancer cells during theranostic process, and the method would open a new avenue for the study of genetically related diseases.