High dielectric constant filler is often used to improve the dielectric properties of polymer. Most studies are focused on the uniform filler dispersion and interface between filler and polymer. Herein, multi-layered films containing BaTiO3 and multi-wall carbon nanotubes (MWCNTs) as fillers, with different filler distributions were designed and prepared, including alternating distribution of layers with/without filler; core-shell distribution with filler concentrated at core or shell; and uniform distribution. The overall filler content in these films was kept constant. These films have almost the same dielectric loss. Interestingly, it was noted that the largest dielectric constant is achieved for sample with filler concentrated at the shell (around 50% higher than the rest at low frequency). Interfacial polarization and filler localization are thought to play important role. However, classic Series model does not take these issues into account. To understand this, a modified Series model was proposed to calculate the dielectric constant of multi-layered films by considering these issues. Such equation is much more accurate at describing experimental results from current study as well as some published literature than classic Series model. Our work demonstrates the importance of hierarchical structure in polymer composites for dielectric property and heterogeneous distribution of filler could be much better than uniform distribution.