Developing an ideal wound dressing material which could accelerate wound closure and achieve scarless wound healing was the ultimate goal of numerous researchers. In this study, biomimetic silk fibroin (SF)/polycaprolactone (PCL) matrices were fabricated via co-electrospinning and positively charged chitosan (CS) and negatively charged type I collagen (COL) were deposited on the nanofibrous mats through electrostatic layer-by-layer (LBL) self-assembly technique. Scanning electron microscopy images indicate that the average fiber diameter of SF/PCL nanofibers became larger and more and more irregular protuberances were observed on their surfaces with the LBL process. Besides, the chemical structure and composition investigation further verified the successful deposition of CS/COL. Additionally, tensile strength and water contact angle tests showed the LBL modified mats had enhanced mechanical properties and good hydrophilicity. Moreover, LBL structured mats acquired excellent antibacterial activity and better ability to promote cell attachment, growth and proliferation. Ultimately, in vivo wound healing assay in rat models revealed that LBL structured mats could reduce the wound closure time, increase collagen production and mitigate excessive scar formation through TGF-β/Smad signaling pathways, which demonstrated the potential application of the nanofibrous mats in skin regeneration.