Mn alloying in thermoelectrics is a long‐standing strategy for enhancing their figure‐of‐merit through optimizing electronic transport properties by band convergence, valley perturbation, or spin‐orbital coupling. By contrast, mechanisms by which Mn contributes to suppressing thermal transports, namely thermal conductivity, is still ambiguous. A few precedent studies indicate that Mn introduces a series of hierarchical defects from the nano‐ to meso‐scale, leading to effective phonon scattering scoping a wide frequency spectrum. Due to insufficient insights at the atomic level, the theory remains as phenomenological and cannot be used to quantitatively predict the thermal conductivity of Mn‐alloyed thermoelectrics. Herein, by choosing the SnTe as a case study, aberration‐corrected transmission electron microscopy (TEM)/scanning transmission electron microscopy (STEM) to characterize the lattice complexity of Sn1.02−xMnxTe is employed. Mn as a “dynamic” dopant that plays an important role in SnTe with respect to different alloying levels or post treatments is revealed. The results indicate that Mn precipitates at x = 0.08 prior to reaching solubility (≈10 mol%), and then splits into MnSn substitution and γ‐MnTe hetero‐phases via mechanical alloying. Understanding such unique crystallography evolution, combined with a modified Debye‐Callaway model, is critical in explaining the decreased thermal conductivity of Sn1.02−xMnxTe with rational phonon scattering pathways, which should be applicable for other thermoelectric systems. Structural evolution induced by Mn alloying is comprehensively investigated in thermoelectric materials, selecting SnTe as a case study. Comprehensive electron microscopy investigations indicate that, through rational structural manipulation, multiscale crystal imperfections are introduced as phonon scattering sources and in turn renders a high thermoelectric performance.