In this paper, we demonstrated a novel physical mechanism based on the well-barrier hole burning enhancement in a quantum well (QW) semiconductor optical amplifier (SOA) to improve the operation performance. To completely characterize the physical mechanism, a complicated theoretical model by combining QW band structure calculation with SOA’s dynamic model was constructed, in which the carrier transport, interband effects and intraband effects were all taken into account. The simulated results showed optimizing the thickness of the separate confinement heterostructure (SCH) layer can effectively enhance the well-barrier hole burning, further enhance the nonlinear effects in SOA and reduce the carrier recovery time. At the optimal thickness, the SCH layer can store enough carrier numbers, and simultaneously the stored carriers can also be fast and effectively injected into the QWs.