Ultrathin (down to 300 nm), high quality carbon molecular sieve (CMS) membranes were synthesized on mesoporous γ‐alumina support by pyrolysis of defect free polymer films. The effect of membrane thickness on the micropore structure and gas transport properties of CMS membranes was studied with the feed of He/N2 and C3H6/C3H8 mixtures. Gas permeance increases with constant selectivity as the membrane thickness decreases to 520 nm. The 520‐nm CMS membrane exhibits C3H6/C3H8 mixture selectivity of ∼31 and C3H6 permeance of ∼1.0 × 10−8 mol m−2 s−1 Pa−1. Both C3H8 permeance and He/N2 selectivity increase, but the permeance of He, N2, and C3H6 and the selectivity of C3H6/C3H8 decrease with further decrease in membrane thickness from 520 to 300 nm. These results can be explained by the thickness‐dependent chain mobility of the polymer film which yields thinner final CMS membranes with reduction in pore size and possible closure of C3H6‐accessible micropores. © 2015 American Institute of Chemical Engineers AIChE J, 62: 491–499, 2016