Si–Ge is a well-known disordered alloy exhibiting high anharmonicity. These two features, disorder and anharmonicity, arise due to the unique nature of bonding instead of structural complexity and are beneficial as they limit the thermal conduction and are widely used in high-temperature thermoelectric applications. In this regard, a comprehensive understanding of the nature of interatomic bonds and the calculation of the Grüneisen parameter, which is a characteristic metric of anharmonicity, of the individual bond are essential to design a crystalline solid along with the development of a high-throughput thermoelectric alloy exhibiting ultralow lattice thermal conductivity. Here, we demonstrate the origin of the low lattice thermal conductivity, κl, of ∼0.8 and 0.4 Wm–1 K–1 for the transition-metal (Ni and Cr)-doped Si–Ge alloy, respectively, due to the difference in the anharmonic pair potential achieved using synchrotron-based X-ray absorption fine structure spectroscopy. The technique enables the determination of the Grüneisen parameter of the individual bond in the alloy and thus reveals the unpaired electron-induced bond anharmonicities and bonding heterogeneity. The technique also determines the bond Grüneisen parameter more precisely in comparison to the values obtained from the speed of sound, as the latter neglects the existence of the soft TO mode, which also contributes to lattice dynamics. Thus, the synergistic presence of (i) heteroatoms as point scatters (mass contrast), (ii) bonding anharmonicities, and (iii) electron–phonon scattering suppresses the lattice thermal conductivity beyond the theoretical alloy limit. Furthermore, the analysis imparts a conception for the estimation of the bond Grüneisen parameter through the acquisition and analysis of extended X-ray analysis of fine structure (EXAFS) spectra.