In this paper, we construct the Möbius domain wall fermions (MDWFs) in the Schrödinger functional (SF) scheme for the SU(3) gauge theory by adding a boundary operator at the temporal boundary of the SF scheme setup. Using perturbation theory, we investigate the properties of several constructed MDWFs, including the optimal type domain wall, overlap, truncated domain wall, and truncated overlap fermions. We observe the universality of the spectrum of the effective four-dimensional operator at the tree-level, and fermionic contribution to the universal one-loop beta function is reproduced for MDWFs with a sufficiently large fifth-dimensional extent.