The Si/Ge single interface and superlattice structure with atom mixing interfaces are constructed. The effects of interfacial atomic mixing on thermal conductivity of single interface and superlattice structures are studied by non-equilibrium molecular dynamics simulation. The effects of the number of atomic mixing layers, temperature, total length of the system and period length on the thermal conductivity for different lattice structures are studied. The results show that the mixing of two and four layers of atoms can improve the thermal conductivity of Si/Ge lattice with single interface and the few-period superlattice due to the “phonon bridging” mechanism. When the total length of the system is large, the thermal conductivity of the superlattice with atomic mixing interfaces decreases significantly compared with that of the perfect interface. The interfacial atom mixing will destroy the phonon coherent transport in the superlattice and reduce the thermal conductivity to some extent. The superlattce with perfect interface has obvious temperature effect, while the thermal conductivity of the superlattice with atomic mixing is less sensitive to temperature.