Carbon nanotube (CNT) fibers exhibit outstanding intrinsic properties, yet their macroscopic performance is often limited by structural disorder, void formation, and collapse during high-temperature processing. Here, we introduce a polymer-scaffold-guided graphitization strategy in which polyimide (PI) functions as a thermally stable scaffold to maintain CNT alignment, suppress collapse, and regulate structural evolution. Upon heat treatment up to 2900 °C, the PI-containing CNT fibers exhibited enhanced graphitic ordering, extended axial correlation length, and reduced interlayer spacing, as confirmed by Raman spectroscopy, small-angle and wide-angle X-ray scattering (SAXS and WAXS). Notably, the CNT/PI fiber with 50% PI content achieved a correlation length of 13.7 nm, leading to exceptional thermal conductivity (534  91 W m-1K-1), electrical conductivity (0.64  0.02 MS m-1), tensile strength (3.26  0.3 GPa) and modulus (870 138 GPa). These findings demonstrate that PI acts not only as a reinforcing polymer but also as a structural scaffold that guides graphitization and directional phonon transport, enabling the design of high-performance, anisotropic CNT-based fibers for thermal management and advanced structural applications.