Stem cells, ideal for the tissue repair and regeneration, possess extraordinary capabilities of multidirectional differentiation and self‐renewal. However, the limited spontaneous differentiation potential makes it challenging to harness them for tissue repair without external intervention. Although conventional approaches using biomolecules, small organic molecules, and ions have shown specific and effective functions, they face challenges such as in vivo diffusion and degradation, poor internalization, and side effects on adjacent cells. Nanoengineered biomaterials offer a solution by solidifying and nanosizing these soluble regulating molecules and ions, facilitating their uptake by stem cells. Once inside lysosomes, these nanoparticles release their contents in a controlled “molecule or ion storm,” efficiently altering the intracellular biological and chemical microenvironment to tune the differentiation of stem cells. This newly emerged approach for regulating stem cell fate has attracted much attention in recent years. This method has shown promising results and is poised to enhance clinical stem cell therapy. This review provides an overview of the design principles for nanoengineered biomaterials, discusses the categories and characteristics of nanoparticles, summarizes the application of nanoparticles in tissue repair and regeneration, and discusses the direction of nanoparticle‐enhanced stem cell therapy and prospects for its clinical application in regenerative medicine.