This paper investigates the propagation of Stoneley waves through bonded and unbonded interfaces between two dissimilar homogeneous transversely isotropic generalized thermo-elastic diffusion rocks. The governing equations for the current problem are obtained and are solved to determine the characteristic polynomial equations for both mediums in terms of penetration depth. These equations are solved using Ferrari’s approach, and the variation in penetration depths with angular frequency and wavenumber is shown. The secular equations of the Stoneley waves are developed using proper boundary conditions and these equations have been solved numerically to determine the phase velocity and attenuation coefficients. We have discovered three modes of the Stoneley waves in thermo-diffusive crustal rocks. We have confirmed that the paths of particle motion for Stoneley waves are elliptic in nature. Some known results [Kumar et al. [2017] “Mathematical modeling of Stoneley wave in a transversely isotropic thermoelastic media”, Applications and Applied Mathematics 12(1), 319–336; Kumar and Kansal [2008b] “Propagation of Rayleigh waves on free surface of transversely isotropic generalized thermoelastic diffusion”, Applied Mathematics and Mechanics29(11), 1451–1462] are recovered from this analysis to validate our investigation.