One of the greatest challenges for advancing lithium-ion battery (LIB) technology is to minimize cell degradation during operation for long-term stability. To this end, it is important to understand how cell performance during operation relates to complex LIB microstructures. In this report, transmission X-ray microscopy (TXM) nanotomography is used to gain quantitative three-dimensional (3D) microstructure-performance correlations of LIB cathodes during cycling. The 3D microstructures of LiMn2O4 (LMO) electrodes, cycled under different conditions, including cycle number, operating voltage, and temperature, are characterized via TXM and statistically analyzed to investigate the impact of cycling conditions on the electrode microstructural evolution and cell performance. It is found that the number of cracks formed within LMO particles correlated with capacity fade. For the cell cycled at elevated temperatures, which exhibits the most severe capacity fade among all cells tested, mechanical cracking observed in TXM is not the only dominant contributor to the observed degradation. Mn2+ dissolution, as verified by detection of Mn on the counter electrode by energy dispersive spectrometry, also contributed. The current work demonstrate 3D TXM nanotomography as a powerful tool to help probe in-depth understanding of battery failure mechanisms, which could be applicable to electrode structure optimization for advancing LIB development.