Dopant‐induced microstructure in thermoelectric materials significantly affects thermoelectric properties and offers a potential to break the interdependence between electron and phonon transport properties. However, identifying all‐scale dopant‐induced microstructures and correlating them with thermoelectric properties remain a huge challenge owing to a lack of detailed microstructural characterization encompassing all length scales. Here, the hierarchical boron (B)‐induced microstructures in B‐doped Si80Ge20 alloys with different B concentrations are investigated to determine their precise effects on thermoelectric properties. By adopting a multi‐scale characterization approach, including X‐ray diffraction, scanning and transmission electron microscopy, and atom probe tomography, five distinctive B‐induced phases within Si80Ge20 alloys are identified. These phases exhibit different sizes, compositions, and crystal structures. Furthermore, their configuration is comprehensively determined according to B doping concentrations to elucidate their consequential impact on the unusual changes in carrier concentration, density‐of‐states effective mass, and lattice thermal conductivity. The study provides insights into the intricate relationship between hierarchical dopant‐induced microstructures and thermoelectric properties and highlights the importance of investigating all‐scale microstructures in excessively‐doped systems for determining the precise structure‐property relationships.