Novel silicon oxide nanojunction structures with various shapes, such as X type, Y type, T type, ringlike and treelike, are fabricated in a self-assembled manner by the hydrothermal method without any metallic catalyst. In the silicon oxide nanojunctions, both the silicon oxide nanowire part and the junction part consist of the same chemical composition, forming homogeneous homojunctions and being made suitable for application in nanoscale optoelectronics devices. The formation of silicon oxide nanojunctions may be influenced by the surrounding environment in the reaction kettle, growth space among the silicon oxide nanowires and the weight of SiO droplets at the growth tip.