We report synergistic co-assembly between smectic A liquid crystal (SmA LC) and planar anchoring fluorosilane functionalized silica (F-SiO2) nanoparticles (NPs). Both scanning electron microscope (SEM) images and grazing incidence X-ray diffraction (GIXD) patterns show that when cooled from the isotropic phase to SmA phase, F-SiO2 NPs (100-500 nm in diameter) migrate from the bottom to the top of the LC film through the central cusp defects of toric focal conic domains (TFCDs). When the NPs form a monolayer on top, replacing the LC/air interface, vertically aligned SmA layers are formed between the top and bottom planar surfaces. When F-SiO2 NP diameter is small (<500 nm), we observe a weak-anchoring regime, where NPs do not cause appreciable layer curvature and NP migration is driven by surface energy. When F-SiO2 particle diameter > 500 nm, strong distortions occur in the smectic layers, and the particle is found suspended at the TFCD defect core. The knowledge of the intermediate states of the NP/LC hybrid structures will provide valuable insights to assemble functional nanomaterials such as quantum dots and metallic NPs in an anisotropic medium, and take advantage of their collective assembly behaviors to create more complex and dynamic structures.