High harmonic generation(HHG) driven by intense frequency-comb laser fields can be dramatically enhanced via multiphoton resonance by tuning the carrier-envelope phase(CEP) shift, without increasing the driving intensity. However,the multiphoton-resonant enhancement(MRE) factor in the realistic atomic hydrogen is much smaller than that in a twolevel system. To study the deviation, we present a theoretical investigation of the multiphoton resonance dynamics of three-level systems driven by intense frequency-comb laser fields. The many-mode Floquet theorem(MMFT) is employed to provide a nonperturbative and exact treatment of the interaction between the quantum system and the laser fields. The investigations show that the dipole interaction of a two-level system with the third level affects the multiphoton resonance dynamics and enhances the HHG spectra. It is the dipole interaction of the excited level of the two-level system with other levels that results in the smaller MRE factor in the realistic atomic system. High harmonic generation (HHG) driven by intense frequency-comb laser fields can be dramatically enhanced via multiphoton resonance by tuning the carrier-envelope phase (CEP) shift, without increasing the driving intensity. However, the multiphoton- resonant enhancement To study the deviation, we present a theoretical investigation of the multiphoton resonance dynamics of three-level systems driven by intense frequency-comb laser fields. The many-mode Floquet theorem (MMFT) is employed to provide a nonperturbative and exact treatment of the interaction between the quantum system and the laser fields. The investigations show that the dipole interaction of a two-level system with the third level affects the multiphoton resonance dynamics and enhances the HHG spectra. It is the dipole interaction of the excited level of the two-level system with other levels that results in the smaller MRE factor in th e realistic atomic system.