Traditional epoxy resin (EP) materials have difficulty to meet the performance requirements in the increasingly complex operating environment of the electrical and electronic industry. Therefore, it is necessary to study the design and development of new epoxy composites. At present, fluorinated epoxy resin (F-EP) is widely used, but its thermal and mechanical properties cannot meet the demand. In this paper, fluorinated epoxy resin was modified by ordered filling of fluorinated graphene oxide (FGO). The effect of FGO interlayer spacing on the thermal and mechanical properties of the composite was studied by molecular dynamics (MD) simulation. It is found that FGO with ordered filling can significantly improve the thermal and mechanical properties of F-EP, and the modification effect is better than that of FGO with disordered filling. When the interlayer spacing of FGO is about 9 Å, the elastic modulus, glass transition temperature, thermal expansion coefficient, and thermal conductivity of FGO are improved with best effect. Furthermore, we calculated the micro parameters of different systems, and analyzed the influencing mechanism of ordered filling and FGO layer spacing on the properties of F-EP. It is considered that FGO can bind the F-EP molecules on both sides of the nanosheets, reducing the movement ability of the molecular segments of the materials, so as to achieve the enhancement effect. The results can provide new ideas for the development of high-performance epoxy nanocomposites.