Novel hydrogen-bonded acidic fluorinated poly(amide-imide-silica) hybrid materials, FPAI-SiO2 (6E and 6F) series, were synthesized by a sol-gel process. The structures and spin relaxation of the hybrids were characterized by infrared (IR), and Si-29 and C-13 nuclear magnetic resonance (NMR) spectroscopy. The abundant Q(4) structures implied that in free catalyst the degree of condensation of tetramethoxysilane was enhanced by hydrogen-bonded acidic fluorinated poly(amide-imide). The dynamics on the local mobility of the hybrids was investigated by the time constant for energy exchange between H-1 and Si-29 spin system (T-SiH) and spin-diffusion path length (L) measurements. It was found that the faster T-SiH of 6E and 6F hybrids compared with the previous study of similar 6C and 6D hybrids implied that 6E and 6F hybrids had more aggregated structures even though the organic terminal segment changed from rigid imide to more flexible amide. The interactions of the charge transfer between donor and acceptor molecules or pi-pi aromatic stacking may be the dominant factors to affect the structures of 6E and 6F hybrids. Moreover, M-1 and D-2 segments of 6F hybrids had the same level mobility and the mobility of the 6F hybrids was little improved as the soft and flexible 1,3-bis(3-aminopropyl)-tetramethyl-disiloxane segment was incorporated in the dense structures of 6F hybrids. All of the L values of 6E and 6F hybrids were on the scale of 3.5-4.0 nm. The result also suggested that 6E and 6F hybrids had similar denser structures as 6D hybrids.