Microstructure engineering fulfilled by phase transformation elicits the reduced thermal conductivity κ in thermoelectric materials. We demonstrate that the multiscale hierarchical twinning structure could exist in the GeTe alloys as the phase transformation from cubic β-GeTe to rhombohedral α-GeTe is manipulated by two-step cooling. The coexistence of nanoscale and microscale herringbone structures yields the low-lying κ, attributing to the reorientation of martensitic variants and pile-up of martensitic twinning. Dilute dopants of Cu and Bi/Sb further suppresses hole carrier concentration nH to the order of 1020 cm−3, leading to the enhanced power factor PF = S2ρ−1 of α-GeTe. Meanwhile, the phase diagram engineering probes the solubility limit of Cu in the single-phase GeTe, diminishing the formation of undesired impurity phases. These strategies boost the peak zT value to 1.5 at 698 K in the light-doped Bi0.01Cu0.01Ge0.98Te alloy. The multiscale twin hierarchy and carrier optimization synergistically enhance the thermoelectric performance of GeTe-based alloys that provide a new chapter in search of green energy resources out from phase change materials.