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Flexible graphite film (FGF), as a traditional interface heat dissipation material, has high anisotropy. It is a challenge to enhance both in-plane and through-plane thermal conductivity of FGF. For this reason, the effects of oxygen content, layer spacing, density and particle size on the in-plane and through-plane thermal conductivity of FGF were studied by both molecular simulation and experimental investigation. The simulation results indicate that the ways to improve the thermal conductivity of FGF include reducing oxygen content and layer spacing, increasing the density and matching the size of graphite sheets. The FGF prepared from room temperature exfoliated graphite (RTFGF) has a wide range of adjustable density (1.3–2.0 g/cm3) and thickness (50–400 μm). The thermal conductivity of the RTFGF is significantly improved after heat treatment owing to reduced oxygen content and layer spacing, which is consistent with the simulation results. Moreover, RTFGF with both high in-plane (518 W⋅m−1⋅K−1) and through-plane (7.2 W⋅m−1⋅K−1) thermal conductivity can be obtained by particle size matching of graphite.