Abstract: An isogeometric topology optimization method based on microstructures with high thermal conductivity is proposed in this paper. The thermal conductivity is optimized at the micro scale for a given initial microstructure, and the structure with optimized thermal conductivity is pre-designed by adjusting the weights of the thermal conductivity factors, which ensures a higher degree of design freedom and reduces the computational cost. The isogeometric topology optimization model of the based on optimized microstructure is constructed at the macro scale with the minimum thermal compliance as the optimization objective, which improves the computational accuracy on the base of the accurate model in the isogeometric analysis and ensures the high continuity of the final multiscale structure. Finally, the effectiveness and generalization of the proposed method are demonstrated by two-dimensional and three-dimensional arithmetic examples. The results show that the proposed method can effectively improve the thermal conductivity of multiscale structures and achieve the design of multiscale structures in irregular design domains.