Background: Intestinal ischemia-reperfusion (I/R) injury is a common and severe clinical issue. With high morbidity and mortality, it burdens patients and the healthcare system. Despite the efforts in medical research, current treatment options are unsatisfactory, urging novel therapeutic strategies. Oxidative stress and dysregulated autophagy play pivotal roles in the pathogenesis of I/R injury, damaging intestinal tissues and disrupting normal functions. The aim of this study is to fabricate macrophage membrane-coated manganese dioxide nanospheres loaded with rapamycin [Ma@(MnO₂+RAPA)] for alleviating intestinal I/R injury. Methods: We engineered honeycomb MnO2 nanospheres coated with a macrophage membrane to act as a drug delivery system, encapsulating RAPA. In vitro OGD/R model in IEC-6 cells and in vivo mouse I/R injury models were used. Targeting ability was evaluated through in-vivo imaging system. Effects on cell viability, reactive oxygen species (ROS) levels, oxygen generation, inflammatory factors, apoptosis, autophagy, and biocompatibility were detected by methods such as MTT assay, fluorescence microscopy, ELISA kit, TUNEL assay, Western blotting and histological analysis. Results: In this study, Ma@(MnO₂+RAPA) efficiently deliver RAPA to damaged tissues and exhibited good ROS-responsive release. Our data showed that Ma@(MnO₂+RAPA) reduced ROS, increased O₂, inhibited inflammation, and promoted autophagy while reducing apoptosis in IEC-6 cells. In a mouse I/R model, Ma@(MnO₂+RAPA) significantly reduced Chiu’s score, improved tight conjunction proteins, decreased apoptosis, reduced levels of inflammatory cytokines and oxidative stress. RAPA released from the Ma@(MnO₂+RAPA), enhanced the expression of autophagy-regulated proteins p62, Beclin-1, and LC3II. The biocompatibility and safety of Ma@(MnO₂+RAPA) were confirmed through histological analysis and biochemical detection in mice. Conclusion: Our results demonstrated that Ma@(MnO₂+RAPA) alleviated intestinal I/R injury by reducing oxidative stress, promoting autophagy, and inhibiting inflammation. This study offers a potential therapeutic strategy for the treatment of intestinal ischemia-reperfusion injury.