Mg3Sb2‐based intermetallic compounds with exceptionally high thermoelectric performance exhibit unconventional n‐type dopability and anomalously low thermal conductivity, attracting much attention to the underlying mechanisms. To date, investigations have been limited to first‐principle calculations and thermodynamic analysis of defect formation, and detailed experimental analysis on crystal structure and phonon modes has not been achieved. Here, a synchrotron X‐ray diffraction study clarifies that, against a previous view of a simple crystal structure with a small unit cell, Mg3Sb2 is inherently a heavily disordered material with Frenkel defects, charge‐neutral defect complexes of cation vacancies and interstitials. Ionic charge neutrality preserved in Mg3Sb2 is responsible for exotic n‐type dopability, which is unachievable for other Zintl phase materials. The thermal conductivity of Mg3Sb2 exhibits deviation from the standard T−1 temperature dependency with strongly limited phonon transport due to a strain field. Inelastic X‐ray scattering measurement reveals enhanced phonon scattering induced by disorder. The results will draw renewed attention to crystal defects and disorder as means to explore new high‐performance thermoelectric materials.