The effect of pulse width on near-infrared supercontinuum generation in nonlinear fiber amplifier is investigated theoretically and experimentally. The complex Ginzburg–Landau equation and adaptive split-step Fourier method are used to simulate the propagation of pulses with different pulse widths in the fiber amplifier, and the results show that a longer pulse is more profitable in near-infrared supercontinuum generation if the central wavelength of the input laser lies in the normal dispersion region of the gain fiber. A four-stage master oscillator power amplifier configuration is adopted and the output spectra under picosecond and nanosecond input pulses are compared with each other. The experimental results are in good accordance with the simulations which can provide some guidance for further optimization of the system.