Si-based rechargeable lithium-ion batteries (LIBs) have generated interest as silicon has remarkably high theoretical specific capacity. It is projected that LIBs will meet the increasing need for extensive energy storage systems, electric vehicles, and portable electronics with high energy densities. However, the Si-based LIB has a substantial problem due to the volume cycle variations brought on by Si, which result in severe capacity loss. Making Si-based anodesenabled high-performance LIBs that are easy to utilize requires an understanding of the fading mechanism. Due to its distinct advantage in morphological changes from microscale to nanoscale, even approaching atomic resolution, electron microscopy is one of the most popular methods. Based on operando electron microscopy characterization, the general comprehension of the fading mechanism and the morphology evolution of Si-based LIBs are debated in this review. The current advancements in compositional and structural interpretation for Si-based LIBs using advanced electron microscopy characterization methods are outlined. The future development trends in pertinent silicon materials characterization methods are also highlighted, along with numerous potential research avenues for Si-based LIBs design and characterization.