Characterizing oxide nuclear fuels is difficult due to complex fission products, which result from time-evolving system chemistry and extreme operating environments. Here, we report a machine learning-enhanced approach that accelerates the characterization of spent nuclear fuels and improves the accuracy of identifying nanophase fission products and bubbles. We apply this approach to commercial, high-burnup, irradiated light-water reactor fuels, demonstrating relationships between fission product precipitates and gases. We also gain understanding of the fission versus decay pathways of precipitates across the radius of a fuel pellet. An algorithm is provided for quantifying the chemical segregation of the fission products with respect to the high-burnup structure, which enhances our ability to process large amounts of microscopy data, including approaching the atomistic-scale. This may provide a faster route for achieving physics-based fuel performance modeling.