Scanning probe lithography has been widely integrated into functional device fabrication but often results in coexistence of oxidation and etching owing to complex interfacial reactions, which severely undermine the performance, functionality, and long-term stability of advanced electronics. To date, the transition mechanism between oxidation and etching remains poorly understood, and effective regulation strategies are still lacking. Here, it is revealed that pulsed bias can regulate the competition between ion transport and electron transfer, which plays a decisive role in determining interfacial reaction pathways and enabling selective oxidation or etching. By simply adjusting the pulse parameters, atomic-level oxidation and etching patterns can be achieved on hydrophilic 4H-SiC (0001) surfaces. Density functional theory calculations reveal that bias-driven charge transfer lowers the transition-state energy barrier and weakens the Si–C bonds. Electronic structure calculations further elucidate the kinetics of proposed cathodic electro-enhanced catalytic etching. High-angle annular dark-field scanning transmission electron microscopy images confirm that the underlying lattice beneath the etched regions remains intact with no detectable subsurface damage. This study not only provides theoretical insights into oxidation and etching behaviors at the atomic scale but also realizes their tunable transition through pulse regulation, holding significant implications for the development of advanced wide-bandgap semiconductor devices.