We have studied hydrothermal synthesis of organic-modified metal oxide nanoparticles and found that the assemblies of nanoparticles were formed when we synthesized metal oxide nanoparticles in the presence of organic molecules with two functional groups. The structure of synthesized nanoassemblies was analyzed by scanning electron microscopes (SEM) and other analytical methods. The use of SEM revealed the three-dimensional nanostructure of the assemblies as well as their surface morphology. In this review, we will show how our study on the synthesis of metal oxide nanoparticles was accelerated by the use of SEM.