Phonon engineering, as a commonly used strategy to achieve high thermoelectric performance, typically requires heavy doping to achieve the largely suppressed thermal conductivity. In this work of the Hf‐doped Zr 3 Ni 3 Sb 4 Zintl, we discovered two unconventional mechanisms, namely avoided crossing and phonon softening, which enable a significant reduction in lattice thermal conductivity with only a small amount of Hf doping. DFT calculations reveal that the significant phonon‐rattler scattering induced by the heavy element Hf doping is the physical origin of the occurrence of avoided crossing and phonon softening, which effectively suppress the group velocity at certain frequencies, shorten the phonon lifetime, and significantly increase phonon anharmonicity. Furthermore, Zr 2.75 Hf 0.25 Ni 3 Sb 3.95 Te 0.05 alloy is experimentally identified as the optimal composition. A small amount of Hf drastically lowers the lattice thermal conductivity and marginally decreases the electrical conductivity, leading to the increased average ZT value by 21%. These results highlight the application potential of Zr 3 Ni 3 Sb 4 ‐based alloys during the medium to high temperature range. Meanwhile, this study provides a new and unconventional phonon mechanism for isoelectronic alloying, which can be applicable to other thermal management aspects.