Covalent modification of nanofillers with polymeric chains is believed an efficient method to improve their dispersion and interfacial adhesion in polymer matrix, which both play critical roles in attaining the high heat conducting properties of the polymer composites. However, the facile graft of polymeric chains onto nanofillers through a one-step approach is still faced with large challenges, especially for the chemically inert carbon nanotubes (CNTs), graphene and boron nitrides. In this work, one-step photo-mediated graft polymerization was used to graft PMMA chains onto the fluorinated CNTs (FCNTs) by using C-F bonds as the initiating sites. It was found that covalent functionalization greatly improves the dispersion of FCNTs in PMMA resin by reinforcing the interfacial interaction between them. Owing to the reduced thermal resistance, the thermal conductivity of functionalized FCNTs based composite outperforms the composite filled with virginal FCNTs in the whole range of filler fractions. Moreover, the PMMA functionalization contributes to strengthening the mechanical performances of the composite, and despite the amount of filler, the composites with functionalized FCNTs always show an excellent electrical insulating property.