Carbon molecular sieve (CMS) membranes were fabricated by designing the polyimides with different diamine moiety such as PPD, ODA, BAPP and BDAF to investigate the effects of multiscale structures of precursors on the microstructure and CO2 separation performance of the derived CMS membranes. The multiscale structures of polymeric precursor were characterized and simulated in terms of the characteristic of functional groups, the flatness of repeat units, the conformation of single chains, the packing efficiency of multi-chain network and the fractional free volume (FFV) of bulk polymers. The microstructure and CO2 separation performance of derived CMS membrane were characterized by XRD, TEM and gas permeation measurements. The CO2 permeation behavior of CMS membranes derived from different precursors was analyzed. Results indicated that the multiscale structures of polyimides significantly influenced the microstructure and CO2 separation performance of derived CMS membranes. Increased FFV (or reduced flatness of repeat units) in the precursor results in an increased disorder degree of carbon structure in the derived CMS membranes. The CMS membranes prepared by high FFV polyimide with helical chain conformation showed the looser carbon structure that are beneficial to CO2 transport compared with that prepared by polyimide with rod-like chain conformation. The larger size of the pendant functional groups (i.e. V-(CF3)2 > V-(CH3)2) in polyimide results in higher CO2 permeability of the derived CMS membranes. The BDAF-PMDA derived CMS membrane pyrolyzed at 700 °C show a high CO2 permeability (0.1 MPa of 50/50 mol.% mixed gas feed) of about 3000 Barrer and moderate CO2/CH4 selectivity, which exhibit an attractive application prospect for CO2 separation.