Epitaxial CoFe2O4 (CFO) films with different thicknesses (6–240 nm) were fabricated on (001) SrTiO3 substrates by reactive cosputtering. Microstructure analyses indicate that the surfaces of the CFO films are covered by islands with height from 2.7 to 0.8 nm upon decreasing film thickness from 240 to 6 nm. Magnetic measurement shows that the CFO films exhibit film thickness dependence of anomalous magnetic properties, including two different “magnetic phases” reflected in the magnetization loops, and reduced saturation magnetization and coercivity with decreasing film thickness. Systematic analyses of the microstructure and magnetization loops for the CFO films with different thicknesses imply that the structure defects on the surface and at the interface, together with the antiphase boundaries in the films are responsible for the anomalous magnetic properties of the CFO films.