The main purpose in this paper is a sample preparation of transmission electron microscopy (TEM) for the lithium-ion secondary battery in the form of micro-sized powders. To avoid artefacts of the TEM sample preparation, the use of ion slicer milling for thinning and maintaining the intrinsic structure is described. Argon-ion milling techniques have been widely examined to make the optimized specimen, which makes TEM analysis more reliable. In the past few years, the correction of spherical aberration (Cs) in scanning transmission electron microscopy (STEM) has been developing rapidly, that results in the direct observation with the atomic level resolution not only for the high acceleration voltage but also its deaccelerated voltage as well. Especially, low-kV application has been markedly increased that needs the sufficient-transparent specimen without the structural distortion during the process of the sample preparation. In this study, the sample preparation for the high-resolution STEM observation has been greatly accomplished and investigations of its crystal integrity are carried out by Cs-corrected STEM.