We have investigated the possible mechanisms of phonon scattering by nanostructures and defects in PbTe-X (X = 2% Sb, Bi, or Pb) thermoelectric materials systems. We find that among these three compositions, PbTe-2% Sb has the lowest lattice thermal conductivity and exhibits a larger strain and notably more misfit dislocations at the precipitate/PbTe interfaces than the other two compositions. In the PbTe-Bi 2% sample, we infer some weaker phonon scattering BiTe precipitates, in addition to the abundant Bi nanostructures. In the PbTe-Pb 2% sample, we also find that pure Pb nanoparticles exhibit stronger phonon scattering than nanostructures with Te vacancies. Within the accepted error range, the theoretical calculations of the lattice thermal conductivity in the three systems are in close agreement with the experimental measurements, highlighting the important role of misfit dislocations, nanoscale particles, and associated interfacial elastic strain play in phonon scattering. We further propose that such particle-induced local elastic perturbations interfere with the phonon propagation pathway, thereby contributing to further reduction in lattice thermal conductivity, and consequently can enhance the overall thermoelectric figure of merit.