ZnO nanocrystallites with the average grain size of about 30 nm and a rod-like morphology have been prepared successfully by a novel microwave hydrothermal (M-H) process in a MDS-6 microwave digestion/extraction system. The influential factors, such as [Zn2+] concentrations, filling ratios of the autoclave, concentration ratios of [Zn2+]/[OH-] have been studied in detail under the designated hydrothermal temperature and reaction time. The as-prepared ZnO nanocrystallites were characterized by the means of X-ray diffraction (XRD), field emission scanning electron microscope (FE-SEM) and transmission electron microscope (TEM). It is found that rod-like ZnO nanocrystallites with the average grain size about 30 nm are prepared. As the increase of [Zn2+] concentrations, the size of as-obtained ZnO nanocrystallites firstly decreases, then increases. The size of as-obtained ZnO nanocrystallites firstly decreases, then increases and finally approaches stable with the increases of filling ratio of the autoclave and concentration ratio of [Zn2+]/[OH-]. To get nearly uniform ZnO nanocrystallites, optimal [Zn2+] concentration condition, filling ratio of the autoclave and concentration ratio of [Zn2+]/[OH-] should be kept at 1.6 mol·L-1, 70%, and 1/2, respectively.