Hyaline cartilage regeneration will bring evangel to millions of people suffered from cartilage diseases. However, uncontrollable cartilage fibrosis and matrix mineralization are the primary causes of cartilage regeneration failure in many tissue engineering scaffolds. This study presents a new attempt to avoid endochondral ossification or fibrosis in cartilage regeneration therapy by establishing biochemical regulatory area. Here, SOX9 expression plasmids are assembled in cellulose gels by chitosan gene vectors to fabricate SOX9+ functionalized scaffolds. RT-qPCR, western blot and biochemical analysis all show that the SOX9 reinforcement strategy can enhance chondrogenic specific proteins expression and promote GAG production. Notably, the interference from SOX9 has resisted osteogenic inducing significantly, showing an inhibition of COL1, OPN and OC production, and the inhibition efficiency was about 58.4 %, 22.8 % and 76.9 % respectively. In vivo study, implantation of these scaffolds with BMSCs can induce chondrogenic differentiation and resist endochondral ossification effectively. Moreover, specific SOX9+ functionalized area of the gel exhibited the resistance to matrix mineralization, indicating the special biochemical functional area for cartilage regeneration. These results indicate that this strategy is effective for promoting the hyaline cartilage regeneration and avoiding cartilage fibrosis, which provides a new insight to the future development of cartilage regeneration scaffolds.