Scar inhibition of dermal equivalent is one of the key issues for treatment of full thickness skin defects. To yield a bioactive RNAi functionalized matrix for skin regeneration with inhibited scarring, collagen-chitosan/silicone membrane bilayer dermal equivalent (BDE) was combined with trimetylchitosan (TMC)/siRNA complexes which could induce suppression of transforming growth factor-β1 (TGF-β1) pathway. The RNAi-BDE functioned as a reservoir for the incorporated TMC/siRNA complexes, enabling a prolonged siRNA release. The seeded fibroblasts in the RNAi-BDE showed good viability, internalized the TMC/siRNA complexes effectively and suppressed TGF-β1 expression constantly until 14 d. Application of the RNAi-BDE on the full-thickness skin defects of pig backs confirmed the in vivo inhibition of TGF-β1 expression by immunohistochemistry, real-time quantitative PCR and western blotting during 30 d post surgery. The levels of other scar-related factors such as collagen type I, collagen type III and α-smooth muscle actin (α-SMA) were also down-regulated. In combination with the ultra-thin skin graft transplantation for 73 d, the regenerated skin by RNAi-BDE had an extremely similar structure to that of the normal one. Our study reflects the latest paradigm of tissue engineering by incorporating the emerging biomolecule siRNA. The 3-D scaffolding materials for siRNA delivery may have general implications in generation of bioactive matrix as well.