Three Zintl phase compounds belonging to the CaYb4Al2Sb6-xGex(x = 0.2, 0.5, 0.7; nominal compositions) system with various Ge-doping contents were successfully synthesized by arc-melting and were initially crystallized in the Ba5Al2Bi6 -type phase (space group Pbam, Pearson codes oP26). However, after post-heat treatment at an elevated temperature, the originally obtained crystal structure was transformed into the homeotypic Ca5Ga2Sb6 -type structure according to powder and single-crystal X-ray diffraction analyses. Two types of crystal structures share some isotypic structural moieties, such as the one-dimensional anionic chains formed by L[Al2Sb8] and the void-filling Ca-2(+)/Yb2+ mixed cations, but the slightly different spatial arrangements in each unit cell make these two structural types distinguishable. This series of title compounds is originally investigated to examine whether anionic p-type doping using Ge can successfully enhance thermoelectric (TE) properties of the Yb-rich CaYb4Al2Sb6-xGex series even after the phase transition from the Ba5Al2Bi6 -type to the Ca5Ga2Sb6 -type phase. More interestingly, we also reveal that the given structural transformation is triggered by the particularly different site-preference of Ca2+ and Yb2+ among three available cationic sites in each structure type, which is significantly affected by thermodynamic conditions of this system. Band structure and density of states analyses calculated by density functional theory using the tight-binding linear muffin-tin orbital method also prove that the Ge-doping actually increases band degeneracies and the number of resonant peaks near the Fermi level resulting in the improvement of Seebeck coefficients. Electron localization function analyses for the (0 1 0) sliced-plane and the 3D isosurface nicely illustrates the distortion of the paired-electron densities due to the introduction of Ge. The systematic TE property measurements imply that the attempted anionic p-type doping is indeed effective to improve the TE characteristics of the title CaYb4Al2Sb6-yGey system.