With the rapid development of nanoscience and nanotechnology, various types of functional nanoreactors have been designed for diverse applications. Here, the recent evolution of the rational design of nanoreactors for chemical synthesis and biomedical applications are briefly summarized and discussed. The presence of nanoreactors provides constrained space isolated from the surrounding environment. Scientists are committed to studying changes in chemical reactions when the reaction system is confined to the nanosized space. Nanoreactors accelerate the reaction rate and even change mechanism of some chemical reactions. Cells and organelles as natural nanoreactors are also discussed. The development of intracellular synthesis makes it possible to realize various applications in biomedicine. The challenges on the rational design of nanoreactors and perspectives are also discussed.