To investigate the prognostic value of minimal residual disease (MRD) detected by multi-parameter flow cytometry (MFC) in pediatric patients with acute myeloid leukemia (AML) after induction chemotherapy. A retrospective study was conducted on 97 pediatric patients initially diagnosed with AML at Wuhan Children's Hospital from August 2015 to December 2022. The study analyzed the results of MRD detection using MFC after the first and second cycles of induction chemotherapy, and its association with prognosis were analyzed. Following the first cycle of induction treatment, 57 of the 97 patients tested positive for MRD (MRD1+ , 58.8%). Subsequently, 19 patients remained MRD positive (MRD2+ , 19.6%) after the second cycle of induction treatment. Kaplan-Meier survival analysis showed that the estimated 3-year overall survival (OS) rate of the 37 (64.9%) MRD1+ patients who underwent transplantation was significantly higher than that of the 20 (35.1%) MRD1+ patients who did not undergo transplantation (84.6% vs 40.0%, P =0.0001). Among the 35 MRD1+ MRD2- patients, the 3-year OS rate of the 25 children who underwent transplantation was higher than that of the 10 children who did not undergo transplantation (87.2% vs 70.0%, P =0.3229). The 3-year OS rate of the 19 MRD1+ MRD2+ patients was lower than that of the 35 MRD1+ MRD2- patients (57.4% vs 81.8%, P =0.059). In the 19 MRD2+ patients, the 3-year OS rate of the 12 children who underwent transplantation was significantly higher than that of the 7 children who did not undergo transplantation (80.8% vs 14.3%, P =0.0007). There was no significant difference in 3-year OS between the 12 MRD1+ MRD2+ patients and 25 MRD1+ MRD2- patients, both treated with transplantation (80.8% vs 87.2%, P =0.8868). In those not treated with transplantation, the 7 MRD1+ MRD2+ patients had a significantly lower 3-year OS compared with the 10 MRD1+ MRD2- patients (14.3% vs 70.7%, P =0.0114). Further multivariate analysis indicated that MRD2 positivity and transplantation were both independent prognostic factors (P =0.031, 0.000), while MRD1 positivity was not significantly associated with the overall prognosis of 97 patients (P =0.902). MRD positivity following the second cycle of induction chemotherapy is an independent risk factor for unfavorable outcomes in children with AML. MRD2 positivity indicates a poorer prognosis and can help to identify the candidates requiring transplantation. MRD2 positivity is not a contraindication for transplantation in pediatric patients, and early transplantation significantly improves the prognosis of high-risk patients.