This work investigates the spatio-temporal evolution of coherent structures in the wake of a generic high-speed train, based on a three-dimensional database from large eddy simulation. Spectral proper orthogonal decomposition (SPOD) is used to extract energy spectra and energy ranked empirical modes for both symmetric and antisymmetric components of the fluctuating flow field. The spectrum of the symmetric component shows overall higher energy and more pronounced low-rank behaviour compared with the antisymmetric one. The most dominant symmetric mode features periodic vortex shedding in the near wake, and wave-like structures with constant streamwise wavenumber in the far wake. The mode bispectrum further reveals the dominant role of self-interaction of the symmetric component, leading to first harmonic and subharmonic triads of the fundamental frequency, with remarkable deformation of the mean field. Then, the stability of the three-dimensional wake flow is analysed based on two-dimensional local linear stability analysis combined with a non-parallelism approximation approach. Temporal stability analysis is first performed for both the near-wake and the far-wake regions, showing a more unstable condition in the near-wake region. The absolute frequency of the near-wake eigenmode is determined based on spatio-temporal analysis, then tracked along the streamwise direction to find out the global mode growth rate and frequency, which indicate a marginally stable global mode oscillating at a frequency very close to the most dominant SPOD mode. The global mode wavemaker is then located, and the structural sensitivity is calculated based on the direct and adjoint modes derived from a local spatial analysis, with the maximum value localized within the recirculation region close to the train tail. Finally, the global mode shape is computed by tracking the most spatially unstable eigenmode in the far wake, and the alignment with the SPOD mode is computed as a function of streamwise location. By combining data-driven and theoretical approaches, the mechanisms of coherent structures in complex wake flows are well identified and isolated.