With the wide application of ultra-microtome sectioning in the preparation of transmission electron microscopy (TEM) specimens with bio- and organic materials, here, we report an ultra-microtome-based method for the preparation of TEM specimens from cathodes of Li-ion batteries. The ultra-microtome sectioning reduces the sample thickness to tens of nanometers and yields atomic resolution from the core region of particles of hundreds of nanometers. Analysis indicates that the mechanical cross-sectioning introduces no observable microstructural artifacts or structural damage, such as microcracking and nanoporosity. These results demonstrate the high efficiency of the ultra-microtome approach in preparing well-thinned specimens of particulate materials that allow for atomic-scale TEM imaging of a large number of sectioned particles in one single TEM specimen, thereby providing statistically significant results of the TEM analysis.