In spontaneous pattern formation by spinodal dewetting, attractive intermolecular forces overcome surface tension and cause an ultrathin liquid film on a low energy substrate to produce ordered structures. Spinodal dewetting in single-layer film on a substrate, is usually manifested by an early stage surface deformation and a highly non-linear ripening stage that results in characteristic morphologies, typically bicontinuous-or hole-like states. Here we have experimentally constructed the dewetting morphology phase diagrams for a bi-layer (Ag, Co) liquid film system on SiO 2 . Nanosecond pulsed laser melting was used to initiate and foster the dewetting as a function of film thickness and arrangement. The early stage ripening morphology was observed by scanning electron microscopy from which the phase diagrams were constructed. Unlike single-layer films, which only show one morphology transition between the bicontinuous to hole states as the film thickness is increased, the bi-layer system can have multiple transitions. We have utilized the thickness-dependent free energy curvature approach (Sharma and Khanna, Phys. Rev. Lett. 81 p3463 1998) to analyze the phase diagram. The location of the multiple transitions cannot be predicted from the curvature minima, as was the case for single-layer films. Nevertheless, despite the complexity from multiple interacting forces and different surface deformation mode in bi-layer systems , the phase diagram can be completely generated by knowledge of the free energy curvature of the respective single-layer films. These results can permit improved modeling of the non-linear dynamics in naturally driven self-organized phenomenon and help design nanomaterials for advanced applications.