We theoretically and experimentally study the polarization and phase control of two-photon absorption in an isotropic molecular system. We theoretically show that the two-photon transition probability decreases when the laser polarization changes from linear through elliptical to circular, and the laser polarization does not affect the control efficiency of two-photon transition probability by shaping the spectral phase. These theoretical results are experimentally confirmed in coumarin 480. Furthermore, we propose that the combination of the laser polarization with the spectral phase modulation can further increase the control efficiency of the two-photon absorption.