Objective: To observe the effect of meisoindigo on apoptosis and proliferation of JAK2/V617F heterozygous mutation cell line-SET2 cell line to further explore the role of JAK-STAT pathway in this effect. Methods: Cell apoptosis after treated with different concentration of meisoindigo (0, 5, and 10 μmol/L) was evaluated by flow cytometry at different time points (24, 48, 72 h). Cell proliferation with CCK8 test was evaluated at different time points (24, 48, 72, 96 h) after administered with different concentration of meisoindigo (0, 5, 10, and 20 μmol/L). After treatment with different concentration of meisoindigo (0, 5, 10, and 20 μmol/L), SET2 cells were collected after 12 h, and then cultured in incomplete methylcellulose-based medium for clone formation. JAK-STAT signaling pathway and apoptosis related protein by Western blot test were evaluated 12 h after administered with different concentration of meisoindigo (0, 5, 10, and 20 μmol/L). Results: At different time points after treated with meisoindigo, the apoptosis rate of SET2 cell lines increased (P<0.01) with the inhibited proliferation (P<0.01), and the decreased clone formation rate of SET2 cell lines [0 μmol/L meisoindigo: (4.48±1.19)%, 20 μmol/L meisoindigo: (2.55±0.36)%; Dunnett P=0.020] in the presence of augmented concentrations of meisoindigo. At 12 hours after administration with meisoindigo, the reduced expressions of JAK2, P-JAK2, P-STAT1, P-STAT3, P-STAT3, STAT5, the decreased anti-apoptosis proteins BCL-2, BCL-XL and the increased pro-apoptosis protein BID, BIM were observed in the presence of increased concentrations of meisoindigo. Conclusion Meisoindigo played an important role during the apoptosis and the inhibition of proliferation in ph-negative myeloproliferative neoplasm cell-SET2 cell lines, which might be related to the inhibition of JAK-STAT signaling pathway with up-regulation of pro-apoptosis protein and down-regulation of anti-apoptosis protein.