The morphological dynamics of electric double layers (EDLs) play important roles in powering next-generation energy devices. However, because the ions and electrodes that form EDLs exist at the nanometer scale, directly observing the behavior of EDLs through experiments remains a considerable challenge. With the rapid advancement of computational modeling, all-atom molecular dynamics (MD) simulations have become a powerful tool, enabling researchers to track the motion of individual atoms and statistically analyze EDL dynamics across various materials and structural environments. In this regard, this review outlines fundamental methodologies employed to study EDL dynamics using MD simulations and explored their practical applications. This work focuses on bridging the gap between observations and simulations at the nanometer, micrometer, and millimeter scales, offering a methodological perspective on multiscale modeling. The establishment of more advanced MD simulation approaches is expected, which would provide an indispensable tool for the design of next-generation soft electrodes and energy conversion devices.