Lithium-based batteries have become the mainstream energy storage system due to their high energy density and long cycle life, driving rapid advancements in smart electronics and electric vehicles. However, the development of lithium-based batteries has encountered several difficult technical challenges, including safety issues and capacity degradation, which result from uncontrollable dendrite growth, complex interface reactions, and volume expansion. There is an urgent need to develop in situ characterization techniques to elucidate the complex evolution processes during battery operation. Small-angle neutron scattering (SANS) serves as a powerful and nondestructive technique to investigate the structural alterations in electrode materials under operational conditions, offering statistical insights into particle morphology and micronanostructure within the multiscale domain of 1–300 nm. Recently, the SANS technique with its distinctive hydrogen–deuterium substitution and contrast variation approach has been employed to monitor the dynamic process in batteries, essentially for mechanism exploration and material design. This review elucidates the application of ex situ/in situ/operando SANS in the realm of lithium-based batteries, offering perspectives for a deeper comprehension of battery performance.