The control of Hg vacancy concentration in HgCdTe grown by MBE with different passivation layer structures was studied. Higher Hg vacancy concentration in HgCdTe was obtained, which provides a basis for the subsequent research and development of new focal plane devices. It was found that the change of Hg vacancy concentration in HgCdTe varies with the structure of passivation layer during thermal annealing. The change is because the existence of the passivation layer of the HgCdTe surface layer changes the equilibrium process of the original thermal annealing. At the same time, the secondary ion mass spectrometry (SIMS) test and the corresponding theoretical fitting were verified the results.