Objective:To explore the clinical features and diagnosis methods of atypical chronic myeloid leukemia (aCML).Methods:The clinical data, bone marrow morphology, immunology, genetics and molecular biology characteristics of a young aCML patient in Nan'an Branch of the Second People's Hospital of Yibin City in Sichuan Province were analyzed.Results:The bone marrow smear showed that 0.875 of the granulocyte system showed obvious proliferation, accompanied by significant dysplasia and immature granulocytosis; blasts accounted for 0.170, and the intracytoplasmic granules of mature granulocytes were significantly increased and thickened. Bone marrow puncture biopsy showed bone marrow hyperplasia was extremely active, immature granulocytes were increased, and reticular fiber was extensively proliferated (marrow fibrosis grade 2-3); biopsy pathology results of left inguinal lymph node showed lymph node structure was destroyed, megakaryocytes and immature granulocytes could be seen in the background of histiocytes, in line with the marrow external hematopoiesis; bone marrow flow cytometry immunophenotype showed granulocyte population accounted for 81.6% of nuclear cells, abnormal expression of CD56 and CD14dim, abnormal growth pattern of granulocyte system; 30 common fusion genes in leukemia screening were negative. Polymerase chain reaction (PCR) method showed BCR-ABL1 fusion gene p210 type, BCR-ABL1 fusion gene p190 type, BCR-ABL1 fusion gene p230 type, CALR gene exon 9, JAK2 gene V617F mutation were all negative. Sanger sequencing showed MPL-W515 gene mutation, CSF3R gene exons 14 and 17, BRAF gene mutation, SRSF2 were all negative. Second-generation sequencing showed ASXL1 gene mutation was positive, NM_015338.5: c.2077C>T (p.R693*) and mutation frequency was 47.7%; U2AF1 gene mutation was positive: NM_006758.2: c.101C>A (p.S34V) and mutation frequency was 51%; PDGFRA, PDGFRB, SETBP1, SF3B1, STAT3, STAT5B were all negative. Karyotype analysis showed 47, XX, add(5)(q33), +8, -10, +mar[8]. The integrated examination was diagnosed as aCML with negative BCR-ABL1.Conclusions:The diagnosis of aCML with negative BCR-ABL1 depends on the comprehensive diagnosis of morphology, immunology, genetics and molecular biology. Second-generation sequencing is particularly important in the differential diagnosis and targeted drug therapy. Early diagnosis and treatment of young patients is extremely challenging and should be paid more attention for clinicians.