Injectable hydrogels are very advantageous in skin tissue-engineering, but generally suffer from several issues including infection, insufficient hair follicle regeneration, and scarring. In this paper, an injectable antibacterial hydrogel is designed for wound healing via integrating antibacterial Ag₂₉ nanoclusters (NCs) and mangiferin (MF) molecules into the 3D network-structured chitosan (CH) hydrogel to eliminate bacterial infection and promote hair follicle/tissue regeneration. This design not only endows the hydrogel with excellent wide-spectrum antibacterial activities, superior biocompatibility, decent injectability, adequate swelling, and good degradability, but also favors the regeneration of capillary vessels/hair follicles/sweat glands for wound healings, which is the “holy grail” of skin tissue engineering. The antibacterial performance of the hydrogel is further improved through the controlled release of Ag species, the formation of a high local concentration of antibacterial Ag species on the hydrogel surface, as well as the capture of bacteria on the hydrogel surface via electrostatic interaction. In vivo experiments reveal that the hydrogel could eliminate bacterial infections and prompt the regeneration of hair follicles/capillaries of wounds, which significantly promotes the skin flap wound healing. This study could shed light on the design of multi-functional Ag NCs-based hydrogel for applications of skin tissue engineering and wound treatments.