The semiconductor optical amplifier (SOA) is simulated by the transmission equation and carrier rate equation of ultrafast nonlinear effects. The effects of carrier density pulsation (CDP), carrier heating (CH) and spectral burning hole (SHB) on SOA output gain and phase are studied respectively. The input pulse peak power and the relaxation time of SOA are changed to simulate the CH gain curve. The result shows that in the ultrafast recovery process, the CH contributes more to the saturated than the SHB effect; the CDP effect produces the slow recovery process. The CDP effect is the main reason for the nonlinear phase shift. The effect of SHB on the phase shift of the probe can be ignored. The contribution of CH to the phase shift can produce about 0.8 rad. The intensity of CH can affect the degree of gain saturation and phase shift, but can′t shorten the ultrafast recovery time. Input pulse energy can change the degree of saturation of the CH gain, and with shorter relaxation time, the peak time of CH effect and the gain of SOA ultrafast recovery time decrease gradually.