The amplifying dynamics of the pulse burst in Yb3+-doped fiber amplifier (YDFA) with high-power pulse pump is numerically analyzed by a finite-difference time-domain (FDTD) method. The numerical simulations show that the amplitude uniformity of the amplified pulse burst can be modified by adjusting the parameters of pump, such as relative delay and power. Though optimizing the pump parameters, we can reduce the gain difference between the pulses in a burst and improve the efficiency of coherent pulse stacking based on Gires-Tournois interferometers (GTIs). These results can be applied to the design of high energy ultra-short pulse amplifiers based on burst-mode amplification and coherent pulse stacking technology.