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We investigate the tunneling dynamics of the Fermi gases in an optical lattice in the Bose–Einstein condensation (BEC) regime. The three critical scattering lengths and the system energies are found in different cases of Josephson os-cillation (JO), oscillating-phase-type self-trapping (OPTST), running-phase-type self-trapping (RPTST), and self-trapping (ST). It is found that the s-wave scattering lengths have a crucial role on the tunneling dynamics. By adjusting the scattering length in the adiabatic condition, the transition probability changes with the adiabatic periodicity and a rectangular periodic patte emerges. The periodicity of the rectangular wave depends on the system parameters such as the periodicity of the adjustable parameter, the s-wave scattering length.