Microstructured materials that can selectively control the optical properties are crucial for the development of thermal management systems in aerospace and space applications. However, due to the vast design space available for microstructures with varying material, wavelength, and temperature conditions relevant to thermal radiation, the microstructure design optimization becomes a very time-intensive process and with results for specific and limited conditions. Here, we develop a deep neural network to emulate the outputs of finite-difference time-domain simulations (FDTD). The network we show is the foundation of a machine learning based approach to microstructure design optimization for thermal radiation control. Our neural network differentiates materials using discrete inputs derived from the materials’ complex refractive index, enabling the model to build relationships between the microtexture’s geometry, wavelength, and material. Thus, material selection does not constrain our network and it is capable of accurately extrapolating optical properties for microstructures of materials not included in the training process. Our surrogate deep neural network can synthetically simulate over 1,000,000 distinct combinations of geometry, wavelength, temperature, and material in less than a minute, representing a speed increase of over 8 orders of magnitude compared to typical FDTD simulations. This speed enables us to perform sweeping thermal-optical optimizations rapidly to design advanced passive cooling or heating systems. The deep learning-based approach enables complex thermal and optical studies that would be impossible with conventional simulations and our network design can be used to effectively replace optical simulations for other microstructures.