The three-dimensional quantitative analysis and nanometer-scale visualization of the microstructural evolutions of a tin electrode in a lithium-ion battery during cycling is described. Newly developed synchrotron X-ray nanotomography provided an invaluable tool. Severe microstructural changes occur during the first delithiation and the subsequent second lithiation, after which the particles reach a structural equilibrium with no further significant morphological changes. This reveals that initial delithiation and subsequent lithiation play a dominant role in the structural instability that yields mechanical degradation. This in situ 3D quantitative analysis and visualization of the microstructural evolution on the nanometer scale by synchrotron X-ray nanotomography should contribute to our understanding of energy materials and improve their synthetic processing.