Background and Purpose: The Bazhen decoction is one of the most extensively used Traditional Chinese medicine (TCM) prescriptions for anti-aging. However, due to the complicity of the components, the pharmacological mechanism of Bazhen decoction is still limited. Experimental approach: We applied RNA sequencing and transcriptome analysis to get the full view of the signaling pathways regulated by Bazhen decoction in the wild type cell background. By using the progeroid cells derived from Werner syndrome mice, we applied Western blot, Immunofluorescence, flow cytometry and telomere FISH to verify the transcriptome data. Key Results: The transcriptome profile revealed that Bazhen decoction might systematically regulate multiple anti-aging pathways, including stem cell regulation, protein homeostasis, cardiovascular function, neuronal function, anti-inflammation, anti-DNA damage induced stress, DNA helicase activity and telomere lengthening. We found that multiple DNA helicases and telomere regulating proteins were up-regulated by Bazhen decoction, which promoted the resolving of G-quadruplex (G4) structure, and facilitated DNA replication and telomere elongation. These improvements also endowed the cellular resistance to DNA damages induced by replication stress. Together these data suggest that Bazhen decoction facilitate G4 resolving and telomere maintenance, which might contribute to the longevity sustaining properties revealed by transcriptome profile. Conclusions & Implications: Our data revealed a new strategy for recovering the pharmacological signature pathways for TCM, which could help the clinical precision medicine of TCM. By applying transcriptome in TCM-treated normal cell, we tried out a systematic analysis for dissecting the molecular mechanism of complicated TCM prescription in the normal genetic background.