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The origin of the intricate nanostructure of La0.5-xLi0.5-xSr2xTiO3 (0.0625 <= x <= 0.25) perovskite-type Li ion conductors has been investigated. Reciprocal space electron diffraction analysis and aberration-corrected STEM by combining annular bright field (ABF) and high angle annular dark field (HAADF) imaging methods have been used to elucidate the complex local atomic arrangements which cannot be adequately described by average crystal structure models. Two different local crystal structures endotaxiallyrelated at the nanoscale without compositional phase separation associated, constituting the crystals. Self-organization of the two different ordered regions arises as a consequence of the competition between two distortive forces in the crystal lattice: octahedral tilting and second-order Jahn-Teller distortion of TiO6 octahedra.