TFDB‐based PIs (BTDA‐TFDB, PMDA‐TFDB and 6FDA‐TFDB) were prepared by the polymerization of 2,2′‐bis(trifluoromethyl) benzidine (TFDB) with three different dianhydrides, which contained flexible carbonyl bridged unit, rigid‐rod moiety without bridged unit, and bulky CF3 bridged unit in dianhydride moieties, respectively. The influence of dianhydride moieties on the aggregate structure and gas permeation performances of polyimide was systematically investigated in relation to their chain packing and free volumes, using the methods of molecular simulation, positron annihilation measurement and X‐ray diffractogram. Changing the dianhydride from benzophenonetetracarboxylic dianhydride (BTDA) to pyromellitic dianhydride (PMDA) and 4,4′‐(hexafluoroisopropylidene) diphthalic anhydride (6FDA), the gas permeation coefficients of polyimide increased, and the gas permeation selectivity (O2/N2, CO2/N2, H2/N2 and CO2/CH4) decreased. With the introduction of flexible carbonyl bridged unit into dianhydride moiety, the high rotational mobility favored tight chains packing and decreased free volumes, which in turn led to the lowest permeation coefficients of BTDA‐TFDB. The bulky CF3 bridged unit in dianhydride moiety greatly restricted chain packing and increased free volumes, thus resulting in the highest permeation coefficients of 6FDA‐TFDB. From BTDA‐TFDB to PMDA‐TFDB and 6FDA‐TFDB, the permeation selectivity decreased. This was mostly ascribed to the reduction of diffusive selectivity, which was resulted from the increase in free volumes.