We theoretically and experimentally demonstrate the control of the intermediate state absorption in (1+2) resonance-mediated multiphoton absorption process by shaping the femosecond laser pulse. A theoretical model is proposed to investigate the intermediate state absorption of (1+2) resonance-mediated three-photon absorption process in the molecular system, and an analytical solution is obtained on the basis of time-dependent perturbation theory. Our theoretical results show that the intermediate state absorption can be enhanced by controlling the laser spectral phase due to final state absorption reduction, and this absorption enhancement efficiency increases with the increase of the laser intensity. These theoretical results are experimentally confirmed in IR144 dye by varying the laser spectral phase with a sinusoidal modulation function.