Abstract Self-healing materials possess the capability to promptly repair minor damages occurring during service, thereby effectively preventing safety accidents. This paper investigates a multi-objective topology optimization method for the macro structure and microtubule network of self-healing materials around pure epoxy resin materials, aiming to enhance the damage healing capability of the microtubule network while meeting the mechanical performance requirements of the macro structure. By introducing the design variables of macro structure and microtubule network, the corresponding topological description functions are established respectively. And study applies logical operations and post-processing techniques to generate an embedded microtubule network structure description. The objective functions include the flexibility of the macro structure, the along-travel head loss, and the total length of the microtubule network, with material volume serving as a constraint. In order to determine the head loss of the three-dimensional microtubule network structure, a Hardy-Cross method based on flow initialization and loop search is proposed. Multi-objective topology optimization is designed based on moving morphable components algorithm, enumeration method and Pareto principle. Develop iterative termination conditions by assessing the disparity between Pareto solution sets in each generation, thereby ensuring algorithm convergence. The numerical example of the Messerschmitt–Bölkow–Blohm (MBB) beamyields a flexibility of 0.059 without a carrier and 0.0728 with a carrier the macrostructural flexibility without a carrier is 81.0% compared to with a carrier, and the macrostructural profiles and the overall flexibility of the MBB beams with/without a carrier are close to each other. This method serves as a reference for optimizing large-scale self-healing structures.