Arrays of epitaxial Fe3O4 nanodots were prepared using laser molecular beam epitaxy (LMBE), with the aid of ultrathin porous anodized aluminum templates. An Fe3O4 film was also prepared using LMBE. Atomic force microscopy and scanning electron microscopy images showed that the Fe3O4 nanodots existed over large areas of well-ordered hexagonal arrays with dot diameters (D) of 40, 70, and 140 nm; height of approximately 20 nm; and inter-dot distances (D int) of 67, 110, and 160 nm. The calculated nanodot density was as high as 0.18 Tb in.(-2) when D = 40 nm. X-ray diffraction patterns indicated that the as-grown Fe3O4 nanodots and the film had good textures of (004) orientation. Both the film and the nanodot arrays exhibited magnetic anisotropy; the anisotropy of the nanoarray weakened with decreasing dot size. The Verwey transition temperature of the film and nanodot arrays with D ≥ 70 nm was observed at around 120 K, similar to that of the Fe3O4 bulk; however, no clear transition was observed from the small nanodot array with D = 40 nm. Results showed that magnetic properties could be tailored through the morphology of nanodots. Therefore, Fe3O4 nanodot arrays may be applied in high-density magnetic storage and spintronic devices.