The system with a film supported by fluid substrate can be widely found in nature and has important applications in engineering fields such as functional surface preparation. This work focuses on the instability mechanism of a fluid-supported inhomogeneous film, and establishes the relationship between geometric and material inhomogeneity and film instability mode. The effects of the length, position and elastic modulus of the defect on the evolution of the film surface instability morphology are studied by numerical simulation. Experiments of the instability of polyester film with prefabricated defects on the water surface are realized by self-designed devices, and the experimental results show that the instability morphology is consistent with the numerical simulation results. By pre-coating the uncured molding gel on the film, the molding gel can copy the instability morphology to form a mold. This work provides not only guidance for the optimal design of the fluid-supported film instability morphology, but also an approach for the preparation of films with specified special morphologies.