In this study, molecular-level mixed matrix membranes are prepared by incorporating two types of carbon quantum dots (QDs), polymer-like QDs (PQD) and graphene oxide QDs (GQD) into Pebax, a poly(ether-b-amide) copolymer. PQD is shown to destroy part of the intrinsic crystalline structure of Pebax as typical fillers do. By comparison, GQD has fewer functional groups and causes an interesting enhancement of the microphase separation of Pebax. The polyether domains become more segregated and more available for the selective CO2 permeation. As a result, the gas separation performance of the membranes is evidently enhanced. GQD outperforms PQD as a filler, and encouraging enhancement occurs at lower loading. The membrane with 0.05 wt % GQD loading shows the optimal gas separation property, while it is 1 wt % for PQD-doped membranes. A possible mechanism is tentatively proposed based on the findings of this study.