Effect of stacking layers on the structure and properties of Ca(Mg1/3Nb2/3)O3/CaTiO3 (CMN/CT) microwave dielectric heterogeneous thin films prepared was investigated. Precursor solutions for CMN and CT synthesis were obtained by Pechini method. The arrangement pattern has affected structure and properties of heterogeneous thin film. The CMN-CT arrangement heterostructure thin film has second phase from the CMN films layer. The CT-CMN heterostructure film which has a smooth and dense microstructure was composed of pure perovskite phase without any second phase, this result was attributed to the CT film layer which is a buffer layer between substrate and CMN film layer. At 1MHz frequency, CT-CMN exhibits the dielectric properties of εr=47.5, tanδ=0.020.