Among the intriguing p-type thermoelectric IV-VI compounds, SnTe is an important alternative to both PbTe and GeTe for free of toxicity of Pb and scarcity of Ge. However, pristine SnTe has poor thermoelectric performance because of its intrinsic high hole concentration, big energy difference between L and Σ bands and high lattice thermal conductivity. In this work, In and Cd co-doping SnTe material, which combines the effect of resonant level and band convergence together, was obtained by self-propagating high-temperature synthesis (SHS) and plasma activated sintering (PAS). The generated Te vacancies are regularly arranged to form super-structured defects in the subsequent constrained hot compressing process, which include regular array of atomic defects and nanoscale precipitates. As a result, the hole concentration of the compressed SnTe-based material is reduced due to the donor doping effect of Te vacancies, and the hole mobility is remarkably improved to 372.94 cm2V−1s−1 and 66.19 cm2V−1s−1 at room temperature for the SnTe and In0.01Cd0.02Sn0.97Te material with compressibility of 35%, respectively. These atomic and nanoscale super-structured defects not only ensure superior electrical transport properties, but also bring much stronger scattering effect on phonons, thus leading to extremely low lattice thermal conductivity of 1.2 Wm−1K−1 at 888 K for the 35% compressed In0.01Cd0.02Sn0.97Te material. With synergistically optimized carrier and phonon transport behavior through resonant level engineering, band convergence engineering and super-structured defects engineering, a peak ZT value of 0.8 is achieved in In0.01Cd0.02Sn0.97Te material with compressibility of 35%. This work provides an effective strategy to realize the decoupling of electron and phonon scattering through Te vacancy-based super-structured defects modulation, and makes up an important part of multiscale microstructure tailoring for thermoelectric materials.