The Liutex core line method, first combined with the snapshot proper orthogonal decomposition (POD), is utilized in a supersonic micro-vortex generator (MVG) wake flow at Ma=2.5 and Reθ=5760 to reveal the physical significance of each POD mode of the flow field. Compared with other scalar-based vortex identification methods, the Liutex core line identification is verified to be the most appropriate approach that is threshold-free and provides full information of a fluid rotation motion. Meanwhile, the Liutex integration is employed to quantitatively track the evolution of the vortices in MVG wake and is applied to the determination of the effective control section of the MVG wake for the optimization study of MVG design. The physical mechanism of each POD mode for multi-scale and multi-frequency vortical structures is investigated by using Liutex core line identification to give some revelations. For the mean mode (mode 0) indicating the time-averaged velocity flow field of the MVG wake flow, a pair of primary counter-rotating streamwise vortices and another pair of secondary vortices is uniquely identified by two pairs of Liutex core lines with Liutex magnitude. In contrast, mode 1 is featured by a fluctuated roll-up motion of streamwise vortex, and the streamwise component of the MVG wake is demonstrated to be dominant in terms of the total kinetic energy contribution. Meanwhile, a dominant shedding frequency of St=0.072 is detected from the temporal behavior of mode 2, which has the organized arc-shaped vortex structures shedding from MVG induced by the K-H instability. Additionally, mode 4 subjects to low-frequency oscillations of the wall vortices and thus takes a relatively lower frequency of St=0.044.