In this work, we investigated the pervaporation separation performance of an ethanol – cyclohexane mixture using a thin-film composite membrane based on a heat-treated, o-hydroxyl-substituted polyimide of intrinsic microporosity (PIM-6FDA-OH). We report in detail the complex chemical and structural transformations that are associated with the development of thermally-rearranged (TR, 400–450 °C), and carbon molecular sieve (CMS) membranes (>500 °C). These transformations strongly affect the affinity-related (e.g. swelling behavior) and morphology-related (e.g. microporosity) properties of the TR and CMS membrane materials which translate into a complex molecular-level separation behavior toward an organic solvent mixture during pervaporation. We show that excellent separation performance (total flux ∼ 4 kg/m2h and ethanol/cyclohexane separation factor of ∼1250) can be achieved after precise thermal treatment at the onset of the CMS formation. In addition, we highlight the unique property of pervaporation where, in contrast to liquid solvent permeation, the downstream side of the membrane remains essentially dry due to exposure to high vacuum. As a result, a sharp molecular cut-off can be achieved within this dry downstream region of the membrane despite considerable overall swelling/penetrant concentration in the upstream region of the membrane.