With the guidance of first-principles phonon calculations, we have searched and found several metastable equilibrium sites for substitutional ferrous iron in MgSiO3 perovskite. In the relevant energy range, there are two distinct sites for high-spin, one for low-spin, and one for intermediate-spin iron. Because of variable d-orbital occupancy across these sites, the two competing high-spin sites have different iron quadrupole splittings (QS). At low pressure, the high-spin iron with QS of 2.3–2.5 mm/s is more stable, while the high-spin iron with QS of 3.3–3.6 mm/s is more favorable at higher pressure. The crossover occurs between 4 and 24 GPa, depending on the choice of exchange-correlation functional and the inclusion of on-site Coulomb interaction (Hubbard U). Our calculation supports the notion that the transition observed in recent Mössbauer spectra corresponds to an atomic-site change rather than a spin-state crossover. Our result also helps to explain the lack of anomaly in the compression curve of iron-bearing silicate perovskite in the presence of a large change of quadrupole splitting, and provides important guidance for future studies of thermodynamic properties of this phase.