Microstructures with engineered properties are critical to thermal management in aerospace and space applications. Due to the overwhelming number of microstructure design variables, traditional approaches to material optimization can have time-consuming processes and limited use cases. Here, we combine a surrogate optical neural network with an inverse neural network and dynamic post-processing to form an aggregated neural network inverse design process. Our surrogate network emulates finite-difference time-domain simulations (FDTD) by developing a relationship between the microstructure’s geometry, wavelength, discrete material properties, and the output optical properties. The surrogate optical solver works in tandem with an inverse neural network to predict a microstructure’s design properties that will match an input optical spectrum. As opposed to conventional approaches that are constrained by material selection, our network can identify new material properties that best optimize the input spectrum and match the output to an existing material. The output is evaluated using critical design constraints, simulated in FDTD, and used to retrain the surrogate—forming a self-learning loop. The presented framework is applicable to the inverse design of various optical microstructures, and the deep learning-derived approach will allow complex and user-constrained optimization for thermal radiation control in future aerospace and space systems.