We investigated the high-order harmonic generation (HHG) process of diatomic molecular ion in non-Born-Oppenheimer approximations (NBOA). The corresponding three-dimensional time-dependent Schrödinger equation is solved with arbitrary alignment angles. It is found that the nuclear motion can lead to spectral modulation of HHG in both the tunneling and multiphoton ionization regimes. The universal redshifts of the whole spectrum are unique in molecular HHG. The spectral width of HHG increases in NBOA. We calculated possible influences on redshifts of HHG in real experimental conditions and found that redshifts decrease with the increase of alignment angles of the molecules and are sensitive to the initial vibrational states. It can be used to extract the ultrafast electron-nuclear dynamics and image molecular structure. It will be instructive to related experiments.
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