Microstructural analyses based on aberration-corrected scanning transmission electron microscopy (STEM) observations demonstrate that low-dimensional CsxBi4Te6 materials, known to be a novel thermoelectric and superconducting system, contain notable structural channels that go directly along the b axis, which can be partially filled by atom clusters depending on the thermal treatment process. We successfully prepared two series of CsxBi4Te6 single-crystalline samples using two different sintering processes. The CsxBi4Te6 samples prepared using an air-quenching method show superconductivity at approximately 4 K, while the CsxBi4Te6 with the same nominal compositions prepared by slowly cooling are nonsuperconductors. Moreover, atomic structural investigations of typical samples reveal that the structural channels are often empty in superconducting materials; thus, we can represent the superconducting phase as Cs1-yBi4Te6 with considering the point defects in the Cs layers. In addition, the channels in the nonsuperconducting crystals are commonly partially occupied by triplet Bi clusters. Moreover, the average structures for these two phases are also different in their monoclinic angles (beta), which are estimated to be 102.3 degrees for superconductors and 100.5 degrees for nonsuperconductors.