We present fully ab initio three-dimensional (3D) calculations of highorder harmonic generations (HHG) of aligned hydrogenmolecular ions, HC 2 , subject to intense linearly-polarized laser pulses. The numerical method is based on the high-precision time-dependent generalized pseudospectral method and the wavelet transform as the tool for time-frequency analysis. We show that the orientation of the molecular axis with respect to the polarization of the laser field strongly affect the electron returning times and below-threshold HHG dynamics. In this study, we find that the short (long) trajectories dominate the emission of below-threshold harmonics when the molecular axis is parallel (perpendicular) to the polarization vector of the laser field.