The effect of time-dependent ionization on two-photon absorption (TPA) cross section of 4,4′-bis (dimethylamino) stilbene molecules is studied, through solving, the Maxwell-Bloch equations using an iterative predictor-corrector and finite-difference time-domain technique. The numerical results show that for a few-cycle femtosecond pulse, the one-step resonant TPA is dominating. The two-photon saturation absorption can be observed. The dynamical TPA cross section is a linearly decreasing function of the input pulse intensity when the input intensity is lower than TPA saturation intensity. TPA cross-section of the medium reduces as the value of photoionization cross section increases at the same propagation distance. The propagation distance has an obvious influence on the TPA cross section. The thickness of the molecular samples thus should be taken into account as measuring the TPA cross section. When the femtosecond pulse is applied to measuring the TPA cross section, conditions for the available analytic expressions are discussed.