The orientation of amorphous regions in pure polymers has been noted to be critical to the enhancement of thermal conductivity (TC), but the available reports are still rather few. Here, we propose to prepare a polyvinylidene fluoride (PVDF) film with a multi-scale framework by introducing anisotropic amorphous nanophases in the form of cross-planar alignments among the in-planar oriented extended-chain crystals (ECCs) lamellae, which show an enhanced TC of 1.99Wm−1K−1in the through-plane direction (K⊥) and 4.35Wm−1K−1in the in-plane direction (K∥). Structural characterization determination using scanning electron microscopy and high-resolution synchrotron X-ray scattering showed that shrinking the dimension of the amorphous nanophases can effectively reduce entanglement and lead to alignments formation. Moreover, the thermal anisotropy of the amorphous region is quantitatively discussed with the aid of the two-phase model. Superior thermal dissipation performances are intuitively displayed by means of finite element numerical analysis and heat exchanger applications. Moreover, such unique multi-scale architecture also results in significant benefit in the improvement of dimensional stability and thermal stability. This paper provides a reasonable solution for fabricating inexpensive thermal conducting polymer films from the perspective of practical applications.