A new method for regulating the time-domain characteristics of pulse fiber amplifier is proposed. According to the basic principle of pulse time-domain waveform distortion in fiber amplifier and the specific requirement in practical application of output pulse, the optimum input pulse required to generate target output pulse is obtained by the stochastic parallel gradient descent (SPGD) algorithm. Several particular output pulses can be generated in numerical simulation, which proves the effectiveness of the proposed method. The input pulse can be changed continually when we use the SPGD algorithm, so that the practical output of fiber amplifier comes close to the target output. The control strategy is easy and the output pulse converges rapidly. Good results can be achieved with the proposed method when we generate the pulses with linear boundaries such as rectangular, M-shaped and triangle pulses, or generate the pulses with curved boundaries such as parabola and ellipse pulses, and the proposed method can be widely applied to generating variety types of target pulses.