© 2019 American Physical Society. ©2019 American Physical Society. To reveal the relationship between microstructural disorder and charge localization dynamics in a van-der-Waals-bonded molecular semiconductor, the electrical properties of field-effect transistors with zone-cast pentacene films were characterized by using in situ micro-Raman spectroscopy to monitor the films' intermolecular and intramolecular vibrations. Transformations from a high-temperature phase with reduced molecular vibration along the long axis that were induced by electron localization in pentacene molecules at the channel interface and transformations from a low-temperature phase with increased molecular vibration that were induced by the electron delocalization were clearly observed under gate-bias stress, photoexcitation, and thermal annealing. Multilayer molecular dynamics simulations revealed that electrons should be localized in each pentacene molecule to stabilize the low-temperature phase and that the intramolecular Raman peak corresponds to the amount of out-of-plane molecular displacement that is most influential to charge localization and mobility reduction induced by fluctuating transfer integrals. We propose a unified picture to describe the relationship between out-of-plane structural disorder and charge localization dynamics in pentacene polymorphs.