In the present work, we succeeded in alternatively depositing inorganic nanoparticles and functionalized DNA bases onto the water/oil interface from the water and oil bulk phases. The ligands used were functional thymines and adenines. Their thiol and phosphate groups were used to cap inorganic nanoparticles and their thymine and adenine groups to alter the surface functionality of the nanoparticles, thus enabling a layer-by-layer growth fashion of nanoparticles at the interface. The multiple particle ligation rendered the resulting nanoparticle films rather mechanically robust. As results, the freestanding asymmetric bilayer and trilayer films, composed of negatively-charged Au, positively-charged CdTe, and/or organic Ag nanoparticles were constructed; their areas were as large as over several centimetres, depending on the sizes of the containers used. Our work should bring up a novel methodology to generate asymmetric multilayer films of nanoparticles with a defined control of electron or charge across the films.