The structures and chemical features of layered compounds BaM2Ge4Ch6 (M = Rh, Ir; Ch = S, Se) synthesized by high-pressure and high-temperature methods have been systematically studied. These compounds crystallize in an orthorhombic phase with space group Pbca (No. 61). These compounds have the remarkable structural feature of M-Ge-Ch pyrite-type building units, stacking with Ba-Ch layers alternatively along the c axis. It is very rare and novel that pyrite-type subunits are the building blocks in layered compounds. Theoretical calculations and experimental results indicate that there are strongly polarized covalent bonds between Ge and Ch atoms, forming heteromolecule-like anions in these compounds. Moreover, Ge atoms in this structure exhibit an unusual valence state (∼+1) due to the tetrahedral coordination environment of Ge atoms along with M and Ch atoms simultaneously.