A fluorinated siloxane was prepared from methyl perfluoro (2-methyl-3-oxahexyl) fluoride (hexafluoropropylene oxide dimer) with N- (β-aminoethyl) -γ- aminopropyltrimethyl oxysilane (KH792), and its structure was confirmed by FTIR and 1H-NMR. Co-curing epoxy resin with fluorinated siloxane and polyetheramine to achieve molecular-level modification of epoxy resin. The various properties of the modified epoxy resin composite material were studied. The results showed that the addition of fluorinated siloxane increased the static water contact angle of the material surface from 72.0° to 103.2°, and the surface energy decreased from (42.08±2.17) mJ/m2 to (20.55±1.45) mJ/m2, the water absorption rate of the material was reduced from 1.75% to 1.38%, which effectively improved the hydrophobicity of the material. The dielectric constant was reduced from 3.83 to 3.63, the thermal decomposition temperature (T5%) of the material was increased from 339 °C to 347 °C, and the tensile and bending mechanical properties were increased by 8.5% and 7.7%, respectively. Since the fluorine element content was only 1% (mass percentage) of epoxy resin, the comprehensive performance of epoxy resin composites was the best. Studies by DSC and DMA showed that a small amount of modifier could promote the curing reaction of epoxy resin and improve curing degree and cross-linking density, when the addition of fluorinated siloxane increased, significant microphase separation occurred inside the material and the performance gradually decreased.