Objective To study the clinical features and prognosis of children with acute megakaryocytic leukemia (AMKL) and the clinical effect of acute myeloid leukemia 03 (AML03) regimen for the treatment of pediatric AMKL. Methods The clinical data were collected from 47 children with AMKL who were diagnosed from May 2011 to December 2019. The treatment outcomes and prognostic factors were analyzed. The Kaplan-Meier method and the log-rank test were used for survival analysis. Results Among the 47 children with AMKL, 22 with non-Down syndrome-AMKL were treated by the AML03 regimen, with a median follow-up time of 11.4 months. For the 22 non-Down syndrome-AMKL patients, the remission rate of bone marrow cytology was 85% and the negative rate of minimal residual disease (MRD) was 79% after induction Ⅱ, with a 2-year overall survival (OS) rate of (50±13)% and a 2-year event-free survival (EFS) rate of (40±12)%. The group with positive immunophenotypic marker CD56 had significantly lower 2-year EFS and OS rates than the group with negative CD56 (P 0.05). Conclusions Children with AMKL tend to have a low remission rate and a poor prognosis. Positive immunophenotypic marker CD56, bone marrow cytology during early treatment response, and MRD results are important factors influencing the prognosis. Allogeneic hematopoietic stem cell transplantation has no significant effect on the prognosis of AMKL.