To attain thermally conductive but electrically insulating polymer films, in this study, polyimide (PI) nanocomposite films with 1–30 wt% functionalized hexagonal boron nitride nanosheets (BNNSs) were fabricated via solution casting and following imidization. The microstructures, mechanical and thermal conductive properties of PI/BNNS nanocomposite films were examined by taking account of the relative content, anisotropic orientation, and interfacial interaction of BNNS and PI matrix. The scanning electron microscopy, X‐ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and X‐ray diffractometry data revealed that BNNSs with hydroxy and amino functional groups have specific molecular interactions with PI matrix and they form stacked aggregates in the nanocomposite films with high BNNS loadings of 10–30 wt%. The tensile mechanical strength/modulus, thermal degradation temperatures, and thermal conductivity of the nanocomposite films were found to be significantly enhanced with increasing the BNNS loadings. For the nanocomposite films with 1–30 wt% BNNS loadings, the in‐plane thermal conductivity was measured to be 1.82–2.38 W/mK, which were much higher than the out‐of‐plane values of 0.35–1.14 W/mK. The significant anisotropic thermal conductivity of the nanocomposite films was found to be owing to the synergistic anisotropic orientation effects of both BNNS and PI matrix. It is noticeable that the in‐plane and out‐of‐plane thermal conductivity values of the nanocomposite film with 30 wt% BNNS were ~1.31 and ~3.35 times higher than those of neat PI film, respectively.