Micro vortex generators (mVGs) control cavitation by altering the boundary layer flow structure. This study employs the wall-adapting local eddy-viscosity large eddy simulation (WALE-LES) turbulence model combined with the Zwart–Gerber–Belamri cavitation model to conduct transient numerical simulations on the National Advisory Committee for Aeronautics 0015 baseline hydrofoil and the hydrofoil equipped with mVGs under various cavitation numbers. The proper orthogonal decomposition method and experiments verify the accuracy and consistency of these simulations regarding cavity scale. The study elucidates mechanisms by which mVGs suppress cloud cavitation at low cavitation numbers and induce vortex cavitation at high cavitation numbers. Results indicate that mVGs maintain sheet cavitation characteristics at low cavitation numbers, reducing wall pressure fluctuations and enhancing flow stability. During cavitation inception, mVG-induced vortex cavitation leads to early cavitation formation. In the sheet cavitation phase, modal energy distribution is more dispersed, while in the inception phase, energy is concentrated with significant dominant modes. Moreover, the counter-rotating vortices generated by mVGs mitigate flow separation, enhance leading-edge flow attachment stability, and reduce high-frequency vibrations caused by bubble shedding. This study significantly advances the understanding of cavitation control by accurately simulating and revealing the cavitation control mechanisms of mVGs across different stages using the WALE-LES model. The findings demonstrate that mVGs can effectively stabilize cavity structures at low cavitation numbers, reducing flow instabilities and enhancing overall hydrofoil performance. These insights will have a significant impact on the design of hydrofoils and the development of cavitation control strategies.