Chromatographic media with synchronously large protein adsorption capacity and high processing flux are highly desired in protein separation; however, the creation of such materials still faces enormous challenges. Herein, a robust strategy to develop highly carboxylated monolithic media by combining nanofibrous aerogels' forming technique and an in situ modification approach is reported. The obtained ion-exchange nanofibrous aerogels (IENFAs) exhibit a unique cellular structure consisting of flexible ceramic nanofibers and a functional polymer wrapping layer, endowing them with outstanding underwater superelasticity and compressive fatigue resistance (nearly no plastic deformation after 1000 compressive cycles). Benefiting from the interconnected nanofibrous cellular structure, good hydrophilicity, high carboxylation, and excellent mechanical properties, the IENFAs exhibit synchronously promoted static (2.9 × 10 3 mg g −1 ) and dynamic (1.7 × 10 3 mg g −1 ) lysozyme adsorption capacities and improved buffer flux (2.17 × 10 4 L m −2 h −1 , gravity driven), which are superior to these reported nanofibrous materials and commercial ion-exchange membranes. The IENFAs also possess outstanding performance stability, easy operation, and excellent regenerability. Moreover, the IENFA-packed column could directly and continuously separate lysozyme from egg white solely driven by gravity, highlighting their excellent practical application performance. This work may provide a new avenue to design and develop next-generation high-performance chromatographic media for bioseparation.