Semiconductor quantum dots (QDs), as high-performance materials, play an essential role in contemporary industry, mainly due to their high photoluminescent quantum yield, wide absorption characteristics, and size-dependent light emission. It is essential to construct well-defined micro-/nano-structures using QDs as building blocks for micro-optic applications. However, the fabrication of stable QDs with designed functional structures has long been challenging. Here, we propose a strategy for three-dimensional direct lithography of desired QDs within a hybrid medium with specific protection properties. The acrylate-functionalized hybrid precursors enable local crosslinking through ultrafast laser-induced multiphoton absorption, achieving sub-100 nm resolution surpassing the diffraction limit. The printed micro-/nano-structures possess thermal stability up to 600 °C, which can be transformed to inorganic architectures with a volume shrinkage. Due to the encapsulated QDs within the densely silicon-oxygen molecular networks, the functional structures demonstrate good stability against ultraviolet irradiation, corrosive solutions, and elevated temperatures. Based on hybrid 3D nanolithography, bicolor multilayer micro-/nano-structures are manufactured for applications in 3D data storage and optical information encryption. This research presents an effective strategy for the fabrication of desired QD micro-/nano-structures, supporting the development of stable functional device applications.