In order to research the phenomenon of spontaneous emission in fiber laser, the numerical model of master oscillator power amplifier (MOPA) systerm is established based on the energy-level structure and rate equation of Yb3+-doped fiber. The analysis results by numerical calculation show that the system energy storage and amplified spontaneous emission (ASE) of amplifier are influenced by the pump power and particle population. The ASE is extremely serious in amplifying process with a low repetition rate. To reduce the ASE, continuous pump is changed to pulse pump, which means that a period of pump pulse that recovers the upper-level population adequately is set before the signal pulse. The ASE existing continuously in continuous pump system could be reduced obviously without influencing the signal pulse amplification. Numerical simulation shows that this method is feasible with a suitable pulse width and pump power, furthermore, the result of corresponding experiment agrees well with the calculation result.