A series of polyimide (PI) composite films were prepared using PI as matrix and boron nitride (BN) and aluminum nitride (AlN) as the doped phases. The modification of the thermal conductive filler particles was characterized by Fourier transform infrared (FTIR). The results showed that the silane coupling agent KH550 was successfully coated on the surface of BN and AlN. X-ray photoelectron spectrometer characterization was used to further prove that silane coupling agents were successfully attached to BN and AlN surfaces, forming a new chemical bond. Scanning electron microscope (SEM) was used to analyze the dispersion of filler particles in the matrix. It was found that agglomeration phenomenon occurred when the content of BN particles were high, but this problem was improved after the surface modification of BN. The breakdown field strength and volume resistivity of PI/BN composite film increased first and then decreased with the increase of BN content and reached the maximum when the volume fraction of BN was 5%, which was 191.53 kV/mm and 8.832 × 1013 Ω·m, respectively. When the BN content was 9 vol%, the thermal conductivity of the PI/BN composite film was 0.496 W/(m·K), which was 1.4 times larger than that of the pure PI film. The thermal conductivity of the PI/BN/AlN composite film at the BN and AlN contents of 5 vol% and 1 vol%, respectively, is 0.144 W/(m·K) higher than that of 7 vol% PI/BN. It indicated that the synergistic effect of the composite fillers played a significant role, and at the same time, under the premise of ensuring higher thermal conductivity, the amount of thermally conductive particles could be reduced to some extent. After the surface modification of the filler particles, the properties of the composite film showed the same trend compared with the unmodified one, while the only difference was that there was a certain increase in the numerical value.