Poly(ethylene oxide)- (PEO-) based block copolymer membranes have great potential for use in CO2 separation because of their excellent selectivity and moderate permeability. Whereas numerous studies have focused on the permeation performance of such membranes, the influence of the microphase-separated structures on the gas transport is not well understood. This study examined the phase structure of PEO-polyamide (PA) (commercial name, Pebax) block copolymer membranes by scanning probe microscopy (SPM) imaging and thermal analysis. The membranes with the irregular and more disordered phase-separated structure, such as Pebax-1074 membranes, that had longer PA chains and were made using a faster sol-to-gel transition process resulted in higher CO2 permeability than the membranes with the more ordered phase structure. The CO2 solubility coefficient profile as a function of pressure in the Pebax membranes with dual-mode sorption characteristics indicated the involvement of a glassy hard phase in CO2 transport, particularly at low pressure. The effects of temperature on gas transport and separation performance for a CO2/N-2 gas mixture were also investigated.