The effect of wetting layer transition, including leakage and Auger capture processes, on Rabi oscillation decoherence process in semiconductor quantum dots is analyzed theoretically. The population dynamic equations of a quantum dot interacting with the wetting layer are deduced, and they fit well with the experimental result. The effect of pure dephasing on Rabi osciuation decoherence process is comparatively analyzed. The calculation results show that the simple intensity-dependent damping factor of pure dephasing can well describe the decoherence properties of complex multi-level system.