Atomic-level investigations of the underlying phonon and thermal transports of strongly anharmonic alloy-based thermoelectric materials and their structural phase transitions are yet to be fully explored. Herein, we systematically investigate the anharmonic lattice dynamics and thermal transport of SnS0.75Se0.25 using perturbation theory up to quartic anharmonicity and molecular dynamics simulations with the first-principles-based machine-learning potential. We find the non-monotonic temperature dependence of the phonon linewidths and frequencies of the Γ4 and Y1 modes. This work demonstrates an apparent κL reduction from SnS to SnS0.75Se0.25, mainly attributed to the enhanced scattering rates of the middle-frequency phonons and the decreased group velocities of the high-frequency phonons. We also find that the effects of the quartic anharmonicity on the thermal transport of SnS and SnS0.75Se0.25 are significant, and the phonon coherence contributions are non-negligible in describing the thermal transport. Moreover, we reveal a decrease of κL in SnS0.75Se0.25 by randomizing Se atoms, which can be ascribed to an additional phonon scattering arising from sublattice mass disorder. Display omitted •The non-monotonic temperature dependence of the phonon linewidths and frequencies of the Γ4 and Y1 modes of SnS0.75Se0.25 across the structural phase transition.•An apparent κL reduction from SnS to SnS0.75Se0.25, mainly attributed to the enhanced scattering rates of the middle-frequency phonons and the decreased group velocities of the high-frequency phonons.•A decrease of κL in SnS0.75Se0.25 by randomizing Se atoms, which can be ascribed to an additional phonon scattering arising from sublattice mass disorder.