Abstract: Aiming at the difficulty of multiscale topology optimization to achieve the structural design in irregular design domains, an isogeometric topology optimization method based on microstructures with high thermal conductivity is proposed. At the microscale, the thermal conductivity of commonly used microstructures in multiscale topology optimization was optimized. By adjusting the thermal conductivity weighting coefficients, the structures with better thermal conductivity could be pre-designed, which ensured a high degree of design freedom and reduced the computational cost. At the macroscale, the mathematical model of isogeometric topology optimization based on the optimized microstructure was constructed with the optimization objective of minimum thermal compliance. The final multiscale structure was obtained by updating the macro design variables with the sensitivity analysis scheme. Based on the accurate model in isogeometric analysis, the computational accuracy was improved and the high-order continuity between the elements of the final multiscale structure was achieved. The optimization results of classical rectangular and 2D/3D half annulus heat dissipation structures show that the proposed method can obtain the multiscale structure with a maximum reduction of 7.97% in thermal compliance, which effectively improves thermal conductivity. In addition, the proposed method is applied to irregular structures with different boundary conditions, which demonstrates the applicability in optimizing the thermal topology of complex design domains.