The hexagonal phase of MoO3 is attractive for electrochemical applications owing to its arrangement of atoms, which offers a large number of intercalation sites. The number of intercalation sites also depends on the orientation of the specific crystallographic plane. In this report we present a facile and low cost method to synthesize the metastable hexagonal phase of MoO3 containing NH4+ and H2O in the form of nanorods (pyramidal and prismatic) using a thiourea synthesis. The unique hexagonal phase of MoO3 was realized using a single step solvothermal process. In this work, thiourea provides the ammonium ions which alter the growth rate and stabilize the hexagonal framework. The morphology of the resulting samples changes from pyramidal to prismatic when the thiourea concentration is increased. The phase compositions and the morphologies of the as prepared samples were investigated by X-ray diffractometry, thermogravimetric analysis, X-ray dispersive spectroscopy and Field emission scanning electron microscopy, respectively. On the basis of our findings, we propose a growth model with plausible growth mechanisms to account for their formation process.