Nanomaterials are increasingly being employed for biomedical applications, necessitating a comprehensive understanding of their degradation behavior and potential toxicity in the biological environment. This study utilizes a continuous flow system to simulate the biologically relevant degradation conditions and investigate the effects of pH, protein, redox species, and chelation ligand on the degradation of iron oxide nanoparticles. The morphology, aggregation state, and relaxivity of iron oxide nanoparticles after degradation are systematically characterized. The results reveal that the iron oxide nanoparticles degrade at a significantly higher rate under the acidic environment. Moreover, incubation with bovine serum albumin enhances the stability and decreases the dissolution rate of iron oxide nanoparticles. In contrast, glutathione accelerates the degradation of iron oxide nanoparticles, while the presence of sodium citrate leads to the fastest degradation. This study reveals that iron oxide nanoparticles undergo degradation through various mechanisms in different biological microenvironments. Furthermore, the dissolution and aggregation of iron oxide nanoparticles during degradation significantly impact their relaxivity, which has implications for their efficacy as magnetic resonance imaging contrast agents in vivo. The results provide valuable insights for assessing biosafety and bridge the gap between fundamental research and clinical applications of iron oxide nanoparticles.