The lattice structures of epitaxial Fe3O4 films deposited on MgO were studied systematically using polarized Raman spectroscopy as a function of film thickness, where interesting phenomena were observed. Firstly, the spectral conflict to the Raman selection rules (RSRs) was observed under cross sectional configuration, which can be attributed to the tetragonal deformation in the growth direction due to the lattice mismatch between Fe3O4 and MgO. Secondly, the blue-shift and broadening of Raman peaks evidenced the decrease of the tensile strain in Fe3O4 film with decreased thickness. Thirdly, distinct from the other Raman modes, the lowest T 2g mode exhibited asymmetric lineshape, which can be interpreted using the spatial correlation model. The increased correlation length introduced in the model can well explain the enhanced peak asymmetry feature with decreasing thickness. These results provide useful information for understanding the lattice structure of epitaxial Fe3O4 film.