Background: The susceptibility of children with Down syndrome to acute myeloid leukemia especially acute megakaryocytic leukemia (AMKL) is much higher than that of general population. The origination of ML-DS (Myeloid leukemia associated with Down syndrome) cells, the occurrence, development and tumor heterogeneity of ML-DS are still [ambiguous](javascript:;). For children with DS, the incidence of non-AMKL ML-DS is relatively rare, and there is little research on the pathogenesis of this type of leukemia. Methods: Our study for the first time using single-cell RNA sequencing (Sc-RNA seq) technology to analyze the transcriptome of peripheral blood tumor cells from patients with non-AMKL type ML-DS. Transcriptome analysis of 2202 peripheral blood cells from one patient with non-AMKL ML-DS were conducted, and the genetic characteristics of leukemia cells were examined in detail. Results: We reveal that LMO4, CPA3, RAD21, POU2F2, KIT, and ANXA1 were highly expressed in cluster 0, which exhibited heightened stem cell characteristics. During the differentiation of various tumor cell clusters, the expression levels of CPA3, FCER1A, HPGD, HPGDS, LAPTM5, and LMO4 exhibited significant difference during the differentiation of different tumor cell clusters. KEGG pathway enrichment analysis shows that aml-0 subsets are significantly enriched in microRNAs in cancer pathway, which play a key role as post transcriptional regulators in leukemogenesis. Conclusion: Above all, the differential gene expression characteristics of different tumor cell subpopulations of interest were analyzed at the single cell level to the heterogeneity of tumor cells and the different characteristics of subpopulations, and to discover potential cell stem gene markers.