Nanoparticles of crystalline molybdenum oxide were prepared by changing the flow rate of plasma gas (2% oxygen balanced by Ar) using an atmospheric-pressure microplasma technique. The morphology and crystalline structure of the nanoparticles were characterized by field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM). The FESEM results revealed that the shape of the deposited nanoparticles depended on the plasma gas flow rate. The TEM results supported the FESEM observations. The transmission electron diffraction (TED) pattern revealed that the obtained nanoparticles changed from MoO2 to MoO3 with the flow-rate increase, and correspondingly the nanoparticle size drastically decreased. A process mechanism is proposed from the observations of optical emission spectroscopy (OES) during the process and consumed wire surface analysis from x-ray photoelectron spectroscopy (XPS) and FESEM studies.