When phonons transport across a material interface, they experience reflection, transmission and mode conversion, which results in a local temperature jump at interface and thus dramatically changes the thermal conductivity of nanostructured materials. Phonon transmission across lattice-matched interfaces has been studied extensively in recent years with the atomistic Green's function (AGF) approach, which usually uses one unit cell to represent the cross-section along the interface. However, modeling phonon transmission across realistic material interfaces is much more challenging because realistic interfaces are usually latticemismatched ones with atomic reconstruction, defects, and species mixing, which demands a larger cross-sectional area for the AGF simulation. In this paper, an integrated molecular dynamics (MD) and AGF approach is developed to study the phonon transmission across latticemismatched interfaces. MD simulation is used to simulate atomic reconstruction close to the 1 Email: Ronggui.Yang@Colorado.Edu interface. The recursive AGF approach is then employed for the first time to calculate frequencydependent phonon transmission across lattice-mismatched interfaces with defects and species mixing, which addresses the numerical challenge in calculating phonon transmission for a relatively large cross-sectional area with reduced computational cost. The study of the relaxed interface formed from two semi-infinite bulk materials shows that lattice mismatch increases the lattice disorder and decreases the adhesion energy, which in turn lowers phonon transmission and reduces the interface thermal conductance across lattice-mismatched interfaces. Low-frequency phonons can be significantly scattered by increasing the defect size across the interface while high frequency phonons can be scattered almost completely (phonon transmission <0.1) across an alloyed layer as thin as 2.27 nm. The effect of lattice-mismatch on phonon transmission becomes smaller for interfaces with defects and species mixing. The effect of annealing temperature on the Si/Ge interface thermal conductance was studied. A significant reduction of the Si/Ge interface thermal conductance was observed for a lattice-mismatched interface when annealed at high temperature, which agrees well with the available experimental data in literature.