Battery decay and failure depend strongly on the solid electrolyte interphase (SEI), a surface corrosion layer that forms on the surface of all battery electrodes. Recently, we revealed the atomic structure of these reactive and sensitive battery materials and their SEIs using cryoelectron microscopy (cryo-EM). However, the SEI nanostructure’s fundamental role and effect on battery performance remain unclear. Here, we use cryo-EM to discover the function of two distinct SEI nanostructures (i.e., mosaic and multilayer) and correlate their stark effects with Li metal battery performance. We identify fluctuations in crystalline grain distribution within the SEI as the critical feature differentiating the mosaic SEI from the multilayer SEI, resulting in their distinct electrochemical stripping mechanisms. Whereas localized Li dissolution occurs quickly through regions of high crystallinity in the mosaic SEI, uniform Li stripping is observed for the more ordered multilayer SEIs, which reduces Li loss during battery cycling by a factor of three. This dramatic performance enhancement from a subtle change in SEI nanostructure highlights the importance of cryo-EM studies in revealing crucial failure modes of high-energy batteries at the nanoscale.