Fluorine-containing polyimide (PI) with low dielectric constant (ε) value was firstly synthesized by a polycondensation reaction of 4, 4-(hexafluoroisopropyl) diphthalic anhydride (6FDA), 1, 3, 4-triphenyldiether diamine (APB) and 1, 3-bis(3-aminopropyl) tetramethyldisiloxane (GAPD). γ-glycidoxypropyltrimethoxysilane (KH-560) and aminopropylisobutyl polyhedral oligomeric silsesquioxane (NH2-POSS) were synchronously performed to functionalize the surface of boron nitride (f-BN) fillers, which were then utilized as thermally conductive fillers to fabricate the corresponding f-BN/PI composites. NH2-POSS was successfully grafted on the surface of BN fillers. All the f-BN/PI composites presented better thermal conductivities, dielectric and thermal properties than those of BN/PI composites at the same addition of BN fillers. The obtained thermal conductivity coefficient (λ) of the f-BN/PI composites with 30 wt% f-BN was 0.71 W/mK, higher than that of BN/PI composites with 30 wt% BN (λ of 0.69 W/mK). Modified Hashin-Shtrikman model demonstrated that f-BN possessed relatively lower thermal resistance with PI matrix. Meantime, the corresponding ε and dielectric loss tangent (tanδ) value of the f-BN/PI composites was decreased to 3.32 and 0.004, respectively, lower than that of BN/PI composites with 30 wt% BN (ε of 3.77 and tanδ of 0.007). Moreover, the corresponding heat resistance index (THRI) and glass transition temperature (Tg) of the f-BN/PI composites was further enhanced to 280.2oC and 251.7oC, respectively.