Fe-57 nuclear magnetic resonance (NMR) of magnetite nanocrystals ranging in size from 7 nm to 7 ym is measured. The line width of the NMR spectra changes drastically around 120 K, showing microscopic evidence of the Verwey transition. In the region above the transition temperature, the line width of the spectrum increases and the spin-spin relaxation time decreases as the nanocrystal size decreases. The line-width broadening indicates the significant deformation of magnetic structure and reduction of charge order compared to bulk crystals, even when the structural distortion is unobservable. The reduction of the spin-spin relaxation time is attributed to the suppressed polaron hopping conductivity in ferromagnetic metals, which is a consequence of the enhanced electron-phonon coupling in the quantum-confinement regime. Our results show that the magnetic distortion occurs in the entire nanocrystal and does not comply with the simple model of the core-shell binary structure with a sharp boundary.