This study proposes a deep learning architecture for automatic modeling and optimization of multilayer thin film structures to address the need for specific spectral emitters and achieve rapid design of geometric parameters for an ideal spectral response. Multilayer film structures are ideal thermal emitter structures for thermophotovoltaic application systems because they combine the advantages of large area preparation and controllable costs. However, achieving good spectral response performance requires stacking more layers, which makes it more difficult to achieve fine spectral inverse design using forward calculation of the dimensional parameters of each layer of the structure. Deep learning is the main method for solving complex data-driven problems in artificial intelligence and provides an efficient solution for the inverse design of structural parameters for a target waveband. In this study, an eight-layer thin film structure composed of SiO2/Ti and SiO2/W is rapidly reverse engineered using a deep learning method to achieve a structural design with an emissivity better than 0.8 in the near-infrared band. Additionally, an eight-layer thin film structure composed of 3 × 3 cm SiO2/Ti is experimentally measured using magnetron sputtering, and the emissivity in the 1-4 µm band was better than 0.68. This research provides implications for the design and application of micro-nano structures, can be widely used in the fields of thermal imaging and thermal regulation, and will contribute to developing a new paradigm for optical nanophotonic structures with a fast target-oriented inverse design of structural parameters, such as required spectral emissivity, phase, and polarization.