Block copolymer-stabilized iron oxide nanoaggregates were fabricated into pH-responsive polymeric microspheres for intestinal delivery of the magnetic nanoaggregates. A diblock copolymer consisted of methoxy poly(ethylene glycol) (mPEG) and poly(e-caprolactone) (PCL) was synthesized by ring-opening polymerization. Microspheres, consisted of Eudragit L100-55 encapsulate and stabilized magnetic nanoaggregates, were prepared by an oil-in-oil emulsification technique. The magnetization of the microspheres decreased, and the stability of the magnetic nanoaggregates in aqueous solutions increased as the amount of block copolymers in the microspheres increased. The encapsulated magnetic nanoaggregates were visualized by scanning electron microscopy and energy-dispersive X-ray spectroscopy. The encapsulation efficiency of nanoaggregates of the microspheres increased as the amount of diblock copolymer in the nanoaggregates was increased. The in vitro experiments confirmed the pH-dependent release of the nanoaggregates from the microspheres. The microspheres were administered to the animals by oral gavages, and the nanoaggregates in small intestines were visualized by histological examination of intestinal inner walls. Higher amounts of the block copolymer in the nanoaggregates increased the uptake efficiency in the intestinal tissues. Thus, the incorporation of the block copolymers in the magnetic nanoaggregates increased the intestinal absorption of the aggregates and Eudragit microspheres and effectively protected the nanoaggregates at low pH conditions of the stomach area.