We investigate the third order harmonic generation for model atoms interacting with intense short laser pulses. We focus on the cases where the ponderomotive energy is not big enough to generate high-order harmonics, and where resonant transitions between bound states are also as important as multi-photon ionization and low-order harmonic generation. We find that the third order harmonic intensity from a model hydrogen atom can decrease as the laser frequency draws near a resonance between bound states. We explain this result by looking into the ionization and Rabi oscillation from the numerical calculation of the time-dependent 1-D Schrödinger equation. In order to support our explanation we also investigate the populations of bound states that play an important role in this atomic process.