Electrodialysis is a promising technology for waste acid recovery with the advantages of low energy consumption and high efficiency. In this work, two nucleobase-modified highly sulfonated poly(ether ether ketone) with adenine (SPEEK-50A) and thymine (SPEEK-50T) were successfully synthesized. Then, a series of blending SPEEK-50Ax/50Ty membranes with varying molar ratios of these two functionalized SPEEKs were fabricated by solution casting. The hydrogen bonding crosslinked structure of ‘A-T base pairs’, as well as the acid-base interactions between the incorporated nucleobases and SO3H groups of the polymer backbone, not only enhanced the mechanical properties and thermal stability of the blending membranes, but more importantly, it successfully addressed the over-swelling issue of highly sulfonated SPEEK membrane. The SPEEK-50Ax/50Ty membranes exhibited tensile strengths between 59.3 and 72.3 MPa, which is 2.2–2.6 times that of the pristine SPEEK membrane. And the water uptake of the blending membranes reduced from 116 % to 14.6–19.2 %, while the swelling ratio decreased from 27.1 % to 5.86–6.60 %. The proton affinity of the multiple basic N atoms in nucleobases, as well as the ‘A-T base pairs’ hydrogen bonding network and acid-base interactions between nucleobases and SO3H groups, all can serve as effective proton transport channels. Additionally, the charge repulsion effect of protonated nucleobases and the crosslinking structure is beneficial to the permselectivity. Therefore, the fabricated blending SPEEK-50Ax/50Ty membranes exhibited superior H+ flux (1.66–1.73 mmol m−2 s−1) and enhanced H+/Fe2+ permselectivity (40.3–43.2). The SPEEK-50A0.5/50T0.5 membrane demonstrated a H+ flux of 1.70 mmol m−2 s−1 and a H+/Fe2+ permselectivity of 43.2, which is 2.8 times that of the pristine SPEEK membrane, surpassing both commercially available and recently reported membranes. Therefore, the nucleobase-modified blending SPEEK-50Ax/50Ty membranes might be potential candidates for the efficient recovery of acid from pickling wastewater.