Silicon nanocrystals (Si NCs) with unique optical and electronic properties have been extensively studied due to their potential application in advanced devices such as optoelectronic devices and nano-flash memories. The optical and electronic properties of Si NCs are dependent on composition, number density, Si NCs' size, and so on [1]. Therefore, it is highly desirable to make clear these information of Si NCs. Atom probe tomography (APT) is a powerful tool to study materials with atomic scale resolution, with which the 3D atom map of materials can be reconstructed. In this research, the composition, number density, and size of Si NCs were investigated by APT. With respect to number density and size of Si NCs, the APT results were compared with plan-view TEM.