Background: cartilage damage is a chronic disease that affecting most aging population, and the effects of Chinese herbal formulation combined with bone mesenchymal stem cells (BMSCs) in repairing rat cartilage tissues were tested. Methods: Forty SD rats were randomly divided into group A, B, C and D groups (n=10). A cartilage tissue injury models by surgical drilling was made in rats. The histological and morphological changes of cartilage tissues in each group were evaluated through H&E staining and pathological Mankin scores were also analyzed. Results: our data showed that the combination of herbal formulation and BMSCs implanted 3D bioscaffold can produce most ideal therapeutic effect to repair the damaged cartilage tissue. Mankin scores were significantly decreased at 8 weeks after surgery in each group (P < 0.05). The load-displacement, stress-strain, elastic modulus, and relative expression levels of type II collagen and proteoglycan were significantly increased (P<0.05) in groups D compared to other groups. Conclusion: our data provides novel insights of Chinese herbal formulation combined implanted BMSCs with 3D biological scaffold to improve the repair of damaged knee injury in rats, which demonstrated a promising avenue to treat damaged cartilage in the clinic.