The effective removal of zwitterionic fluoroquinolone (FQ) antibiotics with high water solubility in wastewater is a key environmental challenge due to the inefficacy of conventional methods of wastewater treatment. In this work, zwitterionic covalent organic frameworks (Tp-MTABs) were synthesized through a solvothermal route using 5,5′,5″-methanetriyltris(2-aminobenzenesulfonic acid) (MTABs) as a zwitterionic linker and 1,3,5-triformylphloroglucinol (Tp) as neutral knots for efficient uptake of FQ antibiotics. Tp-MTABs compose of regular distributions of sulfonic acids and amines that produce zwitterionic binding sites, which produce complementary ion-pair interactions with zwitterionic FQ antibiotics. The charge on Tp-MTABs facilitates its initial self-exfoliation to few-layered ionic covalent organic nanosheets (iCONs) with controlled surface charge, which exposes more surface ionic sites and phenyl groups toward FQ antibiotics, improving ion-pair and π–π interactions between iCONs and FQ antibiotics. These iCONs with multiple active sites highly facilitated the process of antibiotics adsorption, boosting the adsorption kinetics and improving the selectivity towards FQ antibiotics. Tp-MTABs endows ultrafast adsorption rate (<30 s) of FQ antibiotics (average over 99%). In addition, Tp-MTABs exhibit high selectivity to the removal of FQs in complex systems containing multiple competing organic compounds and high-salinity natural seawater. This work explored the structural and functional design of iCONs for the removal of organic molecules in environmental remediation.