Classic BCR::ABL1-negative myeloproliferative neoplasms (MPNs) encompass essential thrombocythemia (ET), polycythemia vera, and primary myelofibrosis as clonal hematopoietic stem cell diseases. Secondary acute myeloid leukemia (sAML) transformation is inherent in all MPN subtypes, affects patient outcomes, and is frequently associated with the clonal evolution of disease subclones. Targeted next-generation sequencing has identified adverse mutations, including ASXL1, SRSF2, IDH2, and EZH2 mutations, as markers of sAML transformation in MPNs. The treatment options for sAML range from intensive combination chemotherapy to lower-intensity approaches utilizing hypomethylating agents (HMA) and B-cell lymphoma two inhibitors as well as best supportive care. Allogeneic hematopoietic stem cell transplantation (allo-HSCT) represents a potentially curative option for medically fit sAML patients but is also associated with substantial toxicity including acute and chronic graft-versus-host disease (GvHD), and rarely donor-derived leukemia or myelodysplastic syndrome (MDS). Recent advances in single-cell technologies such as single-cell DNA sequencing (scDNA-seq) have facilitated the study of clonal evolution in myeloid neoplasms, including MPNs. However, a comprehensive characterization of the clonal architecture in sAML using cutting-edge single-cell multi-omics analysis remains lacking. This study aims to decipher the clonal architecture in a patient with JAK2 V617F-mutated ET who subsequently developed sAML and donor-derived MDS. Through the application of single-cell multi-omics analysis at multiple treatment time points, we seek to gain in-depth insights into clonal dynamics and genomic alterations associated with disease progression and treatment response. This study has been approved by the Institutional Review Board of MacKay Memorial Hospital, and written informed consent was provided by the patient.