Phonon transport plays a vital role in various applications of molecular crystals, such as vibrational energy transfer in energetic materials during thermally- or shock-induced processes and in radiative cooling through infrared emissions in delignified and densified wood. Unlike inorganic crystals, molecular crystals are generally composed of large numbers of atoms in the repeating cell, a wide variety of force interactions ranging from long range electrostatic and London dispersion to short-range bonds of covalent or ionic character, and an accompanying broad-based vibrational spectrum with optic branches near 100 THz. Here, we examine the behavior of thermal carriers in four materials – silicon, Cs2PbI2Cl2, α-RDX, and cellulose I β– using multiple thermal transport models including the phonon gas, Cahill-Watson-Pohl, Allen-Feldman, and Wigner models. We show that three unusual mechanisms are remarkably present in molecular crystals: 1) wave-like carriers due to coupling of disparate modes are the dominant contributors to thermal transport in some complex crystals, 2) the thermal transport can occur through two, and as many as four, distinct phonon channels with each channel representing coupled modes through which varying degrees of Zener-like tunneling occur, and 3) anisotropy of thermal conductivity in some materials can only occur through direction-dependent tunneling. The mechanisms are responsible for ∼40, 75, and 80% of the total thermal conductivity in Cs2PbI2Cl2, α-RDX, and cellulose I β, respectively. The findings open new directions for controlling thermal transport in materials through chemical functionalization and molecular design principles.