Investigating the intrinsic properties of the Schottky interface between graphene and 3D bulk silicon is crucial. However, the semiconductor technology introduces extra doping and defects in graphene, which significantly disturbs the property of the graphene‐silicon interface. Here, the interface parameters of graphene/n‐Si heterojunction are derived by the damage‐free Hg‐probe capacitance–voltage measurement. Due to its low‐density states, the Fermi level of graphene can be pushed upward, which results in a lower Schottky barrier height (ΦB0) of Hg/graphene/n‐Si (HGS) heterostructure than that of Hg/n‐Si (HS) structure. Additionally, the series resistance (Rs) of HGS becomes lower than that of HS, which can be attributed to the narrowed depletion layer width (WD) and the decreased interface state density (Nit). Furthermore, the frequency characteristic is also investigated. Because of the weak interface state charge trapping–detrapping process and the decreased Nit at high frequency, electrons will accumulate in graphene, and the Fermi level will be pushed up. Hence, the ΦB0 and Rs will decrease with increasing frequency. This study contributes to a deep understanding of the graphene/silicon heterojunction interfaces, which is crucial for designing and optimizing the new electronic and optoelectronic devices based on 2D/3D heterostructure.