Poly(ether-ether-ketone) (PEEK) is an attractive material for membrane fabrication due to its exceptional thermal and chemical stability. However, traditional PEEK processing necessitates the use of harsh chemicals, such as sulfuric acid because of its limited solubility in organic solvents. To overcome this limitation, copolymers offer a solution by enhancing solubility and subsequently improving membrane characteristics such as permeability and selectivity. Herein, three novel copolymers – PEEK with various contents of SO2 and CH3 – were developed and used in membranes for the separation of polar and non-polar solvents. The chemical structure of the copolymers was tailored by varying the monomer ratio between 0.25 and 0.75 for CH3 and SO2 containing monomers. Diamine–crosslinked PEEK copolymer membranes were prepared using a green solvent (TamiSolve). The effects of the polymer structure, the dope solution rheology, and membrane properties together with separation performance were studied. The resulting membranes demonstrated a permeance for acetonitrile ranging from 7.4 to 8.2 L m−2 h−1 bar−1 with molecular weight cutoffs of 839–915 g mol−1. Molecular dynamic simulations were conducted to explore the interaction between the copolymers and nine different organic solvents. Our findings underscore the significance of copolymer design in achieving tailored membrane properties for diverse separations.