Supercapacitors are highly valued energy storage devices with high power density, fast charging ability, and exceptional cycling stability. A profound understanding of their charging mechanisms is crucial for continuous performance enhancement. Electrochemical quartz crystal microbalance (EQCM), a detection means that provides in situ mass change information during charging–discharging processes at the nanogram level, has received greatly significant attention during the past decade due to its high sensitivity, non-destructiveness and low cost. Since being used to track ionic fluxes in porous carbons in 2009, EQCM has played a pivotal role in understanding the charging mechanisms of supercapacitors. Herein, we review the critical progress of EQCM hitherto, including theory fundamentals and applications in supercapacitors. Finally, we discuss the fundamental effects of ion desolvation and transport on the performance of supercapacitors. The advantages and defects of applying EQCM in supercapacitors are thoroughly examined, and future directions are proposed.