Janus kinase 2 plays a critical role in JAK/STAT signaling pathways, and has a central role in cell cycle.JAK2 have emerged as a novel therapeutic target of myeloproliferative disorders, autoimmune diseases, essential thrombocytosis, and small mol. inhibition of JAK2 activity developed into an impressive drug target.For a series of JAK2 inhibitors pharmacophore model and atom-based 3D-QSAR models have been developed, to identify the essential structural features required for these JAK2 inhibitors using the PHASE module of Schrodinger.A five featured pharmacophore hypothesis with three hydrogen bond acceptors, one hydrogen bond donor and one aromatic ring provided a best atom-based 3D-QSAR model.The developed 3D-QSAR model have good statistical predictive values as R2 = 9659, Q2 = 0.5679 and effective Pearson R = 0.9405.The results illustrate the structural information of substituted aromatic bicyclic compounds containing pyrimidine and pyridine rings, which might be supportive for further rational design of novel potent Janus kinase 2 inhibitors.