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Injectable hydrogel is of interesting for wound healing due to it can be used as carriers of bioactive molecules for the reparation of tissues with minimal invasiveness. However, the integration of lipid-soluble substances into hydrogel network is difficult because of the polarity differences. Here, the tea tree oil (TTO) is encapsulated into the hydrogel network via a previous emulsification process, and a tough and antibacterial injectable hydrogel is synthesized by the Schiff base reaction between carboxymethyl chitosan (CMCS) and genipin (GP). CMCS is served as both an emulsifier and a gel-forming material to construct the heterogeneous hydrogel. The obtained hydrogels present high adhesive strength (∼162.75 kPa), great antibacterial properties (over 90 %) and excellent biocompatibility. Moreover, an anal fistula-like wound healing experiment concluded that the heterogeneous hydrogel has good slow-release properties of TTO for an accelerate healing process, this hydrogel shows great potential for the treatment of complex anal fistula wounds.