Single atom nanozymes (SAzymes) are considered as the most hopeful candidates for replacing natural enzymes. In this work, a flow-injection chemiluminescent immunoassay (FI-CLIA) based on a Fenton-like activity single atom cobalt nanozyme (Co SAzyme) was developed for the rapid and sensitive detection of 5-fluorouracil (5-Fu) in serum for the first time. Co SAzyme was prepared by an in-situ etching method at room temperature using ZIF-8 metal-organic frameworks (ZIF-8 MOFs). With excellent chemical stability and ultra-high porosity of ZIF-8 MOFs as the core, Co SAzyme presents high Fenton-like activity which can catalyze the decomposition of H2O2 to produce large amounts of superoxide radical anions, thus effectively amplifying the chemiluminescence of the Luminol-H2O2 system. In addition, carboxyl-modified resin beads were used as the substrate to load more antigens due to its advantages of good biocompatibility and large specific surface area. Under optimal conditions, the detection range of 5-Fu was 0.001–1000 ng mL−1 with a limit of detection of 0.29 pg mL−1 (S/N = 3). Furthermore, the immunosensor was successfully applied for the detection of 5-Fu in human serum samples with satisfactory results, displaying the potential application of this strategy for bioanalysis and clinical diagnosis.