The development of functional thermoelectric materials requires direct evidence of dopants' locations to rationally design the electronic and phononic structure of the host matrix. In this study, Cs-corrected scanning transmission electron microscopy and energy dispersive X-ray spectroscopy is employed at the atomic scale to identify Cu atoms' locations in a Cu-doped SnTe thermoelectric alloy. It is revealed that Cu atoms in the rocksalt SnTe form solid solutions at both Sn and Te sites, contrary to their electronegativity order and the intentional Cu doping at Sn sites. Cu atoms are also located at the tetrahedral and crowdion sites of the face-centred cubic structure, with varying degrees of correlations. Such high flexibility of Cu atoms in the rocksalt SnTe offers diverse phonon-scattering mechanisms conducive to the ultra-low lattice thermal conductivity of singly Cu-doped SnTe. This study offers atomic-scale insights for achieving more precise dopant engineering, leading to the accelerated development of functional thermoelectric materials.