Mixed matrix membranes (MMMs) have shown great advantages in overcoming the Robeson trade-off effect, and various fillers have been utilized to improve the gas permeation and separation performance. In this study, hollow polypyrrole (PPy) nanospheres with mesoporous shells were synthesized by chemical polymerization using hard template method. The hollow PPy nanospheres with mesoporous shells were investigated by transmission electron microscopy, scanning electron microscopy, Brunauer Emmett Teller and small-angle X-ray scattering. We introduced hollow PPy nanospheres into poly(ether-block-amide) (Pebax1657) as fillers to prepare MMMs for CO2 separation. The effects of the hollow PPy nanospheres on the physical properties and the gas permeation and separation performance were studied. The results showed that the addition of hollow PPy nanospheres contributed to the improvement of the gas permeability. At 1 wt% loading of hollow PPy nanospheres, the MMMs exhibited a highest CO2 permeability of 274 Barrer, which was more than double compared with that of the pure Pebax membrane, accompanied by the slightly increased CO2/N2 selectivity of 40.1 and the slightly increased CO2/CH4 selectivity of 12.8. MMMs with hollow polymer nanospheres display a positive potential application for industrial-scale CO2 separation.