Enrofloxacin (ENR), as a widely used antimicrobial agent in aquaculture, poses potential risks to ecosystems and human health due to its environmental persistence. Therefore, it is of great significance to explore efficient methods for removing ENR from aquaculture wastewater. In this study, a series of shrimp shell-derived aerogel (MBC300–MBC700) were fabricated from Litopenaeus vannamei shells through chemical modification followed by pyrolysis at 300–700 °C, and their adsorption performance and mechanisms toward ENR were systematically investigated. The modified porous materials exhibited a well-developed micro–mesoporous structure, high specific surface area, and abundant surface functional groups. Meanwhile, MBC400 demonstrated the highest adsorption capacity for ENR, reaching 14.56 mg/g, with a corresponding specific surface area of 77.71 m²/g. The adsorption kinetics followed the pseudo-second-order model, and the isothermal data were better fitted by the Freundlich model, indicating a chemisorption-dominated, heterogeneous multilayer adsorption process. Thermodynamic analysis revealed that the adsorption was spontaneous (ΔG < 0) and endothermic (ΔH > 0). In regeneration experiments, 30% ethanol solution achieved the best desorption efficiency for MBC400, with adsorption efficiency remaining above 75% after three cycles. Based on the characterization and adsorption results, adsorption mechanism of ENR on MBC400 was elucidated as a synergistic effect of hydrogen bonding, π–π stacking, electrostatic interaction, and surface complexation. This study provides a novel strategy and theoretical basis for the high-value utilization of shrimp shell waste and for the efficient removal of fluoroquinolone antibiotics from aquaculture effluents.