The performance of resin-based composite materials often exhibits diversity due to the designability of various components. Thermal conductivity, an important thermal parameter of the composite, plays a significant role in thermal-chemical reactions, thermal stress analysis, temperature conduction, etc. However, it is relatively difficult to experimentally explore the thermal conduction mechanism of hybrid composite materials, mainly due to the relatively difficult control of various components. Therefore, this paper proposes a sequentially coupled cross-scale numerical method to characterize the thermal conductivity of nano-reinforced composite materials with pores by a multiscale periodic Representative Volume Element model generated by an improved Random Sequential Absorption algorithm. Firstly, periodic temperature boundary conditions are described, and the thermal conductivity performances of nano-reinforced matrix and composite with pores are investigated based on the finite element homogenization theory. Then, the proposed modes are validated and grid sensitivity analysis is conducted, indicating that the optimal grid sizes for the RVE models are 1.9 nm for the nano-reinforced matrix and 0.14 μm for the composite with pores based on a comprehensive comparison of four pore characterization methods, respectively. Furthermore, the study explored the effect of multiple parameters including nanoparticle content, pore content, and pore shape on thermal conductivity. Numerical findings reveal that the thermal conductivity of the nanocomposite matrix exhibits a linear increase with higher particle content. Specifically, compared to 0 % particle content, the thermal conductivity rises by 141.92 % at 12 % particle content. While the composite material's transverse thermal conductivity is sensitive to porosity content, it is less influenced by pore shape. The method proposed in this paper provides an effective approach for studying the thermal conduction of nano-reinforced composite materials with pores, and the research findings also offer theoretical guidance for process engineers.