•Calculation of cross-scale anisotropic thermal transport in carbon fiber composites.•Use of the dual coordinate system to describe thermal conductivity anisotropy.•The mechanism of interface rotation affecting interfacial thermal resistance.•The heat transport properties of fiber tortuosity and orientation within the resin substrate were investigated. The thermal conductivity parameter of materials is a fundamental factor for thermal management and the study of heat transfer processes. In the present work, we constructed the microscopic topology and interfacial structure of the fiber structure based on the homogenization of finite elements and molecular dynamics theory. For the anisotropy of fiber thermal conductivity, we proposed an anisotropic cross-scale heat transport model for carbon fiber/epoxy resin (CF/ER) composites, with consideration of interfacial thermal resistance (ITR). Based on the numerical validation of the reliability of the method, we established a dual coordinate system to analyze the mechanism of the geometric topological parameters on the structural anisotropic heat transport. The fiber volume fraction significantly affected the effective thermal conductivity (ETC) within a range of 10% to 15%, with ETC growth rates of up to 50%. The fiber orientation angle influenced the main heat transfer direction, and when the fiber volume fraction was 40%, increasing the fiber orientation angle to 90° could enhance the ETC in the axial direction up to 130.28%. Meanwhile, the larger orientation angle could reduce the interfacial phonon heat dissipation and achieve the better phonon transmission effect. The change of fiber structure could effectively modulate the ETC, while the fiber length and cross-sectional shape would have less effect on the ETC. With the introduction of fiber tortuosity, the heat transport could be regulated by changing the tortuosity. Within the variation range of tortuosity from 1 to 3, the ETC regulation of the composite could be achieved from 12% to 42% in the axial direction and 14% to 34% in the radial direction. With increasing curvature, the ETC variation trend became gradually nonlinear. The study serves as a theoretical basis for the preparation and thermal properties evaluation of fiber-reinforced composites.