Nanocomposite materials present attractive properties and are widely employed in various applications. Most of the time, the insertion of nanoparticles in a polymer matrix induces an enhancement of its performances, yet the effect of the filler on the polymerization mechanisms and the glass transition is less often investigated. In the present study, the PFA/silica nanocomposite was studied to highlight the variation of its polymerization behavior, thermomechanical properties and glass transition induced by the presence of a clustered silica nanoparticles network. The structure of nanosilica clusters was studied by thermogravimetric analysis (TGA), Fourier transform infrared spectroscopy (FTIR). The furfuryl alcohol (FA) polymerization was studied via its activation energy variation in the presence of nanosilica clusters and anhydride maleic (MA) that led to some modifications of the polymerization mechanism. An enhancement of thermal stability and an increase of glass transition temperature have been put in relief by dynamic mechanical analysis (DMA) and were correlated to the presence of silica. Finally, the activation energy associated with the glass transition highlighted a change of the polymer chain motion process in the presence of silica.