Membrane separation of CH4 and C2H6 is challenging due to the similar kinetic diameter and chemical affinity. In comparison with other crystalline porous materials, covalent organic frameworks (COFs) possess the advantages of low density, large surface area, tunable pore structure, versatile functionality, and so on, providing the COFs with great potential as separation membranes. Herein, we studied the membrane-based C2H6/CH4 separation performance of 80 two-dimensional imine-linked COFs. Monte Carlo and molecular dynamics simulations were employed to investigate the adsorption and diffusion of gas molecules in the COF membranes. 7 promising COF structures are screened by evaluating the membrane’s selectivity and permeability, and they are found to have small pore size (<20 Å), void fraction (<0.7), and surface area (<8000 m2·g−1) as well as high framework density (>200 kg·m−3). Pore size and framework density are demonstrated to be dominating factors in determining the selectivity and permeability. Based on two typical COFs, COF-LZU1 and NUS-15, grafting hydrocarbons onto the linker and introducing high-carbon additives into the pore can effectively improve the separation performance. Especially, with an appropriate additive concentration, the fullerenes can increase the C2H6/CH4 selectivity by>10 times. This work aims to explore the potential of COFs as membranes for C2H6/CH4 separation, and provides design strategies to optimize the separation performance, which are also applicable to other porous materials.