To analyze the clinical characteristics and prognosis of mixed phenotype acute leukemia (MPAL) in children. The data of 29 children diagnosed as MPAL in the Pediatric Blood Disease Center, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences from January 1, 2005 to December 1, 2019 were collected retrospectively. The morphology, immunophenotypes, cytogenetics, molecular biological characteristics, induction chemotherapy regimen, and prognosis were analyzed. Kaplan-Meier Method was used to draw survival curve. Log-Rank was used for univariate analysis. (1) Among 29 MPAL cases, there were 1 case with KMT2A rearrangement, 1 case with BCR-ABL1, 13 cases with B/myeloid(B-M) type, 12 cases with T/myeloid(T-M) type and 2 cases with acute undifferentiated leukemia. (2) The common immunophenotypes were CD33 (23 cases, 79%), CD34 (25 cases, 86%) and HLA-DR (20 cases, 69%), and CD19 was positive in 17 cases (59%). (3) In molecular genetics analysis, 8 cases were detected to have abnormal gene fusion, including 1 case with MLL-AF4 fusion gene, 1 case with BCR-ABL1 fusion gene, 3 cases with TEL-AML1 fusion gene, 2 cases with WT1 and 1 case with FLT3-ITD. (4) In cytogenetics analysis, 27 cases obtained chromosome karyotypes, including 14 cases with abnormal karyotypes and 10 cases were complex karyotypes. (5) In treatment efficacy analysis, 27 cases received induction chemotherapy and the complete remission(CR) rate was 85%(23/27).The 5-year disease free survival(DFS) rate was (71±10)% and 5-year overall survival(OS) rate was (74±10)%. Thirteen of 14 cases received acute lymphoblastic leukemia(ALL) induction therapy achieved CR, while 10 of 12 cases received hybrid induction therapy achieved CR. No significant difference was found in 5 year-OS rates between cases with ALL induction therapy and hybrid induction therapy ((77±15)% (80±13)%, χ²=0.027,=0.870). MPAL is a rare childhood leukemia and is prone to incorporate complex karyotypes. Induction therapy with ALL or hybrid regimens is a good choice to obtain favorable prognosis.