A theoretical analysis is made on pulse pumped double-clad Yb-doped fiber amplifier based on master oscillator power-amplifier(MOPA). The interaction processes of the pumping pulse, laser pulse and Raman Stokes optical pulse during the fiber amplification have been analyzed. The change of the upper level population density of the gain fiber with the pumping duration is simulated, and the optimal pumping pulse width is found. With the pumping power increasing, the stimulated Raman effect appeared during the amplification process will restrain the signal pulse energy. The signal pulse energy can reach the peak under the optimal pumping power. The effect of the fiber length and core diameter on the optimum pumping power, laser pulse and first-order Stokes optical pulse is analyzed too. Results show that when the pumping power is the optimum, the bigger core and shorter length fiber should be used in the fiber amplifier in order to increase the signal pulse energy and peak power as much as possible.