Epitaxial lithium ferrite (LiFe5O8) films with different thicknesses have been successfully fabricated on SrTiO3 (001) substrates by magnetron sputtering deposition technique. The microstructural and magnetic properties are characterized by advanced transmission electron microscope and magnetic measurement device. It was found that the formation of structural defects can be influenced by the thickness of the film. Apart from the misfit dislocations, the orientation domains form in thinner film and twin boundaries appear in thicker film, respectively, contributing to the misfit strain relaxation in the heterosystem. The magnetic measurement shows that the thinner films have enhanced magnetization and a relatively lower coercive field compared with the thicker films containing the antiferromagnetic twin boundaries. Our results provide a way for tuning the microstructure and magnetic properties of lithium ferrite films by changing the film thickness.