Multiphoton ionization processes in aligned I2 molecules are actively controlled by the homemade pulse shaping system, with which a time-dependent polarization pulse can be generated and controlled. We find a correlation between a femtosecond time-dependent polarization pulse and the production efficiency of evenly or oddly charged molecular ions. We achieve much better controllability of the correlation with a time-dependent polarization pulse than with a pulse having a fixed ellipticity. The results suggest the existence of an unknown tunnel ionization mechanism which is characteristic of a time-dependent polarization pulse. Our experiments point to new directions in optimal control studies with molecular systems, as discussed in the text.