The impurity elements and their occurrence forms in magnetite have good environmental indication significance. Si is one of the common impurities in magnetite. Although there are great differences between Si and Fe in ionic radius, valency, energy effect of replacement and other aspects, both the in-situ composition data of magnetite and the wet chemical analysis data show that, magnetite contains a certain amount of Si (the mass fraction of SiO₂ of magnetite crystals generated in hydrothermal environment can reach 6.19%). In order to explore whether Si can statically exist in magnetite and its specific form, the first principles of density functional theory was used to calculate the formation energy of Si in different positions of magnetite crystal, and the stability of Si in magnetite crystal was studied. The results show that the doping formation energy of replacing octahedral Fe with Si in magnetite is -4.13 eV, and the doping formation energy of replacing Fe in the tetrahedron center is -3.85 eV. It is noteworthy that the formation energy of both the two Fe³⁺ (tetrahedron center) in a magnetite cell are replaced is -8.87 eV. From the perspective of doping formation energy, Si can exist in the center of tetrahedron and octahedron of magnetite, but the structure obtained by replacing all Fe³⁺ in the center of tetrahedron with Si is the most stable.