Magnetic ionic covalent organic frameworks (MiCOFs) integrate the high specific surface area and regular crystalline structure of COFs with precise functional design, and leverage the rapid magnetic separation capabilities of Fe3O4, presenting significant potential in the field of separation technology. Despite their potential, the integration of ionic liquids (ILs) as functional monomers in MiCOFs remains underexplored. This study utilizes ILs previously screened by the conductor-like screening model for realistic solvents (COSMO-RS) to evaluate the impact of IL phase states on the functional design of MiCOFs. Fe3O4@COF-IL and Fe3O4@COF/IL were prepared through chemical bonding and physical coating, respectively, and assessed for their selective adsorption of benzimidazoles (BZDs) from human plasma. Fe3O4@COF-IL, chemically bonded in solid form, exhibited excellent selective adsorption capabilities, increased surface area, and stable recovery rates, resulting in minimal matrix effects and superior trace analysis reproducibility. Fe3O4@COF/IL, with ILs closer to the liquid state as predicted by COSMO-RS, maintained selective adsorption capacity but showed performance variability due to the ease of IL detachment. This research pioneers the task-specific design of MiCOFs and underscores the significant influence of the IL phase state on performance, providing an important strategy for customizing adsorbents for specific separation challenges in chemical engineering.