A series of palladium(II) complexes with nitro- and formylbenzothiacrown-ether derivatives was synthesized. The spatial structure of the complexes was studied by NMR, X-ray diffraction analysis, and quantum chemical calculations (density functional theory). The cavity size and the ligand denticity were found to be crucial factors determining the geometric configuration of the thiacrown-ether complexes. Palladium(II) complexes with benzodithia-12(18)-crown-4(6) ethers were demonstrated to have a cis-configured S2PdY2 fragment (Y = Cl, OAc). In the case of Pd(II) and benzodithia-21-crown-7 ethers, only complexes with a trans configuration of the S2PdY2 fragment form. In the case of Pd(II) and nitrobenzomonothia-15-crown-5 ether, only 2(ligand):1(Pd) complex with trans configuration of the core fragment forms.