The pH-sensitivity and electroactivity of malachite green (MG), a cationic dye, can potentially affect the surface-enhanced Raman spectroscopy (SERS) profile during electrochemical SERS (EC-SERS) analysis. An EC-SERS investigation was performed by acquiring dynamic SERS profiles of MG on Au SERS substrates at various applied potentials to elucidate the electrochemistry of MG at the molecular level. The appropriate EC-SERS potential window of MG, mass and electron transfer modes, and the number of electrons and protons in the redox process were determined by cyclic voltammetry. The EC-SERS parameters (pH and type of supporting electrolyte) were optimized. The highest SERS signal was achieved by chronoamperometry SERS (CA-SERS) and CV-SERS at an applied potential of 0.6 V (vs. Ag/AgCl) using 0.1 M phosphate buffer at pH 4 as the supporting electrolyte. Plausible mechanisms for electrooxidation and SERS signal enhancement were proposed. The oxidized form of MG, conformational changes, and evolution of the adsorption orientation were successfully elucidated using CV-SERS. This study provides molecular-level insight into the adsorption orientation of MG and its oxidized form, which involves aromatic rings with a tilted upright orientation at positive applied potentials. The mechanism of SERS signal enhancement is expounded, which is valuable for developing EC-SERS-based MG sensing.