This paper gives a numerical research on the Nd-doped fiber amplifier nonlinear refractive index and phase changing with the input signal power, pump power, signal wavelength, gain effect and Kerr effect. The results show that when the signal or pump power increases, the nonlinear refractive index is positive for the signal wavelength being smaller than 1064 nm, and negative for the signal wavelength being bigger than 1064 nm. When the signal wavelength hold a certain value, the nonlinear refractive index increases with the pump power. When the pump is low, the gain effect have more influence on the change of nonlinear refractive index, and when the pump is high, the Kerr effect have more influence on the change of nonlinear refractive index, which caused mainly by gain saturation.