Thermal transport across hard-soft interfaces is critical to many applications, such as polymer composites, solar thermal evaporation, and photothermal cancer therapy. In this work, we use wave packets (WP) in molecular dynamics (MD) simulations to study the phonon energy transmission coefficients (ETCs) across different Au-self-assembled monolayer (SAM)-organic liquid interfaces. Three types of thiol SAMs with different terminal groups and chain length heterogeneities are studied, including “-CH3,” “-COOH,” and “hetero” SAMs. Two types of organic liquids, hexamine and hexane, are investigated. When the liquid changes from hexamine to hexane, the Au-CH3 SAM-liquid interfaces show similar ETCs across different phonon modes, since the interactions between nonpolar SAM and different liquids are similar, while the ETCs across the Au-CH3 SAM-liquid interfaces are much higher than those involving bare Au-liquid interfaces. Due to the -COOH functionalization, the Au-COOH SAM-hexamine interface shows the highest ETCs for all phonon modes compared to the other interfaces, which explains why its interfacial thermal conductance (ITC) is also the highest. We find that the Au-hetero-SAM-hexamine interface has higher ETCs in the longitudinal acoustic (LA) modes than the Au-CH3 SAM-hexamine interface; as a result, the ITC of the Au-hetero-SAM-hexamine interface is slightly higher. The ETCs calculated in our WP simulations can interpret the ITCs calculated from our previous MD simulations. Using the mode-resolved ETCs, the ITC contributions for each phonon mode are also calculated. We find that the LA modes play an important role in thermal transport across Au-SAM-liquid interfaces. Results from this WP study will help design interfaces with desirable thermal transport properties.