In this work, we developed a microscopic theory for polariton thermalization via low-energy molecular vibrations coupled to electronic degrees of freedom and derived a simple analytical expression based on the Stokes shift and linewidth of the 0–0 vibronic peak in emission spectra. We calculated the polariton thermalization rate in a practical microcavity structure and provided a recipe for cavity design and the choice of molecular system to achieve the desired thermalization rate. Last but not least, we revealed important temperature dependence that provides a quantitative understanding of the observed thermalization bottleneck effect at low temperature.