The microscopic origins of thermopower have been investigated to design efficient thermoelectric devices, but strongly correlated quantum states such as charge density waves and Mott insulating phase remain to be explored for atomic-scale thermopower engineering. Here, we report on thermopower and phonon puddles in the charge density wave states in 1T-TaS2, probed by scanning thermoelectric microscopy. The Star-of-David clusters of atoms in 1T-TaS2 exhibit counterintuitive variations in thermopower with broken three-fold symmetry at the atomic scale, originating from the localized nature of valence electrons and their interlayer coupling in the Mott insulating charge density waves phase of 1T-TaS2. Additionally, phonon puddles are observed with a spatial range shorter than the conventional mean free path of phonons, revealing the phonon propagation and scattering in the subsurface structures of 1T-TaS2. Microscopic origins of thermopower are investigated to design efficient thermoelectric devices. Here, the authors report thermopower and phonon puddles in the charge density wave states in 1T-TaS2 by scanning thermoelectric microscopy.