Two kinds of isocyanate were used to modify graphene oxide (GO) samples. Then, polyimide (PI) hybrid membranes containing GO and modified GO were prepared by in situ polymerization. The permeation of CO2 and N2 was studied using these novel membranes. The morphology experiments showed that the isocyanate groups were successfully grafted on the surface of GO by replacement of the oxygen-containing functional groups. After modification, the surface polarity of the GO increased, and more defect structures were introduced into the GO surface. This resulted in a good distribution of more modified GO samples in the PI polymer matrix. Thus, the PI hybrid membranes incorporated by modified GO samples showed a high gas permeability and ideal selectivity of membranes. In addition, enhancement of the selectivity due to the solubility of CO2 played a major role in the increase in the separation performance of the hybrid membranes for CO2, although the diffusion coefficients for CO2 also increased. Both the higher condensability and the strong affinity between CO2 molecules and GO in the polymer matrix caused an enhancement of the solubility selectivity higher than the diffusion selectivity after GO surface modification.