The effects of heterogeneous interfaces on the microstructure, the morphology and the dielectric properties of Ca(Mg1/3Nb2/3)O3/CaTiO3(CMN/CT) multilayered(ML) thin film prepared in the layer-by-layer mode with a certain thickness are investigated. According to the experimental results, an equivalent circuit of CMN/CT ML thin film is simulated, and the theoretical formulae of the dielectric constant and loss of thin film are established. The results indicate that CMN/CT ML thin film, in which CT and CMN phases can exist independently, possesses a pure orthorhombic perovskite structure, dense smooth surfaces and intermediate layers at the heterogeneous interfaces, and that the dielectric constant increases and the dielectric loss decreases with the increase in the number of heterogeneous interfaces, and reducing the thickness of the interfacial transition layer is useful to improve the dielectric properties of CMN/CT multilayered thin film.