High-order harmonic generation (HHG) from the molecular ions stretched to large internuclear distances is studied numerically and analytically in this work. We focus on the fine structure of the HHG spectrum related to the contribution of short electron trajectory. In our numerically solving the time-dependent Schrodinger equation (TDSE), we use a trajectory-dependent filtering procedure to separate the short-trajectory contribution from other contributions of long trajectory and multiple returns. Our TDSE results reveal that the short-trajectory HHG spectra of molecular ion with larger internuclear distance show some complex interference structures characterized by some remarkable dips, and that the position of the dip is sensitive to the laser parameters. With a developed model arising from strong-field approximation (SFA), we are able to identify the physical origins of the complex interference structures. In this model considered is the charge-resonance effect which induces the strong coupling between the ground state and the first excited state of the molecular ion at large internuclear distance. In this model, the well-known effect of two-center interference occurs in the form of the canonical momentum instead of the momentum related to the instantaneous velocity of the electron in the general SFA. It is shown that some dips in TDSE results arise from two-center interference of the electronic wave between these two atomic cores of the molecule in the ionization process, while others come from that in the recombination process. These ionization and recombination dips alternately appear in the HHG spectra from the formed complex interference structures. The main differences between the interference effects in the ionization process and the recombination process are twofold. Firstly, in the ionization process, the destructive two-center interference strongly suppresses the forming of the continuum wavepacket, while in the recombination process, the recombination of the rescattering electron with other bound eigenstates with small weights can also contribute to HHG bedsides the recombination of the ground state with the first excited state with large weights. As a result, in TDSE results, the ionization dips are deeper and more remarkable than the recombination ones. Secondly, in the recombination process, the Coulomb acceleration remarkably changes the de Broglie wavelength of the rescattering electron and therefore changes the position of the interference-induced dip. While in the ionization process, the Coulomb potential plays a small role in the interference effect. As a result, the interference dips in the ionization process and the recombination process differ from each other.