Microalgae-based materials have gained significant attention considering their rich resources, cost-effectiveness, and environmental friendliness. Herein, iron-rich microalgae (Chlorella pyrenoidosa, CP) were treated by hydrothermal reaction under alkaline conditions to remove the protoplast and obtain a hollow shell with an FexOy core inside. Then, the iron-rich microalgae-based aerogel (Fe-CP aerogel) was fabricated through a freeze-drying process. The as-prepared Fe-CP aerogel exhibited superior adsorption performance, and the maximum adsorption quantity for Cu2+ could reach 208.3 mg/g due to the synergistic adsorption of the hollow shell of CP cells and FexOy core. The Fe-CP aerogel also possessed super-hydrophilicity and displayed high separation efficiency (over 99%) when used for separating different oil/water emulsions. Moreover, the existence of FexOy endowed the Fe-CP aerogel with photo-Fenton activity, thus exhibiting excellent antifouling performance. The prepared Fe-CP aerogel could be considered an ideal adsorbent, with green, efficient, low-cost, and regenerative properties, and has the potential for the practical treatment of wastewater.