A femtosecond fiber laser system with high average power and short pulse duration is demonstrated,whose oscillator and amplifier are based on an Yb-doped single-polarization large-mode-area photonic crystal fiber (LMA-PCF) with low nonlinearity, high gain and nice environmentally stability. The dependence of the output pulse duration on the pulse energy, duration and chirp of seed light from oscillator and the pump power of amplifier is studied. The fiber laser amplifier generates 16 W average power, corresponding to 320 nJ pulse energy, at 40 W pump power, when the seed light is fixed at 180 mW average power, and the pulse duration is compressed to 39 fs after gratings.