Based on the nonperturbative quantum scattering theory of high-order harmonic generation (HHG) and using the linear combination of atomic orbitals theory of molecular orbitals, we derive the HHG rate formula for molecules. Employing the formula, we study the intensity dependence of the interference effect induced by the molecular structure. We find that the molecular HHG was modulated by the interference not only in the recombination process but also in the ionization process. The location of the interference minimum in HHG shifts to higher energy by a quantity of the ponderomotive energy as the laser intensity increases.