Numerical simulation results and experimental verification on the pulse evolution process in a photonics crystal fiber (PCF) femtosecond laser amplifier with different pump schemes are reported. A model combining rate equations with nonlinear Schrodinger equation, which considers the interaction among non-uniform gain distribution, group velocity dispersion and self-phase modulation within the fiber, is adopted. Compared with the amplification by forward pump scheme, the simulation results show that the amplified femtosecond pulse by backward pump scheme has not only a higher output power but also a narrower pulse duration and spectral width, i.e. a smaller time-bandwidth-product and less nonlinear accumulation. For the verification test, a photonic crystal fiber femtosecond laser amplifier with the two pump schemes is built. The experiment results are consistent with the numerical simulation, and the physical mechanism of amplified pulse evolution dynamics is discussed.