Segmental mixing has been speculated to affect the gas transport properties of phase-separated polyurethanes. However, in most of the studies in this field the effect of this factor has not been independently evaluated. Therefore, in this study, varying the solution casting temperature was utilized to induce changes in the final morphology of the prepared films with similar molecular compositions, and the relevance of changes in segmental mixing within the domains to the changes in gas transport properties were investigated. The films were characterized using small-angle X-ray scattering (SAXS) and ATR-FTIR to observe the changes in segmental mixing and hydrogen bonding, respectively. A new mathematical treatment was developed based on the analysis of invariant in conjunction with one-dimensional correlation function calculated from the SAXS data. This method allows for the comparison of the purity of both hard and soft domains among the prepared samples. The effects produced by varying the casting temperature on the purity of the domains were discussed in detail. Also, gas diffusivity and solubility were found to be significantly affected by the purity of soft domains.