Selective separation of 1-C4H8 and 2-C4H8 isomers is of great importance and a daunting challenge in petrochemical industries because these isomers differ only by the position of the C=C double bond. Here, we proposed that an elliptical nanopore embedded in graphene with a minor diameter of similar to 3.4 A can be a promising candidate to separate 2-C4H8 from 1-C4H8 with ultrahigh selectivity. Inspired by chain structures, we designed a series of elongated pores by connecting several elliptical nanopores in series with one removed benzene ring overlapped. The molecular dynamics studies demonstrated that the elongation design greatly enhances the permeability of 2-C4H8 while maintaining the selectivity of 2-C4H8 over 1-C4H8 to a certain extent. The underlying mechanisms are related to the local size sieving and molecular conformations that the pore prefers. We anticipate our findings can guide the future design of more energyefficient and cost-effective membranes for isomer separation.