One approach using the counterintuitive pulse sequence (CPS) is presented to control the intramolecular hydrogen transfer. We have applied the asymmetric double-well model to the substituted malonaldehyde and have shown the complete population transfer from one local minimum state to another one through the barrier using CPS. We also have found in our simulation that the high product yield is robust with respect to the changes of the laser parameters. The mechanism of the population transfer is elucidated with our approach with the Huckel theory in a systematic and pictorial way.