The local structure and chemical environment critically govern transport properties in quantum and energy materials, but their atomic-scale manifestations remain elusive. Here we uncovered the atomic characteristics, intrinsic origin, and thermoelectric implications of chemical inhomogeneity in
Bi 2 Te 3 -based materials with varying Se alloying. Using aberration-corrected electron microscopy, chemical bonding analysis, and thermodynamic modeling, we revealed pronounced Se enrichment in the central layer of a quintuple structure and constructed precise atomic models for this intrinsic inhomogeneity. Atomic-scale charge-density and valence-state measurements provided direct experimental evidence for chemical bonding disparity in
Bi 2 Te 3 , with more covalent bonding in central layers and greater ionic bonding in outer layers. We also showed that this bonding disparity, coupled with entropy-enthalpy competition, drove the observed site preference and local chemical segregation in
Bi 2 Te 3 − x Se x (
x = 0.5 , 1.0, 1.5, 2.0, and 2.5). The site-resolved bonding analyses further demonstrated that selective Se occupation tuned both ionic and covalent components of Bi–
X bonds in
Bi 2 Te 3 − x Se x . Therefore, this intrinsic chemical inhomogeneity modulated bonding polarity, the electronic band gap, and the Seebeck coefficient, serving as a fundamental determinant of thermoelectric performance. Our findings highlight atomic-scale chemical inhomogeneity as a key factor in tailoring functional properties of layered quantum materials beyond thermoelectrics.