Exosomes are nanosized membrane-bound extracellular vesicles with the capacity to modify functions and behaviors of recipient cells via transferring unique biological information. Mounting evidence suggests that under developmental conditions, mesenchymal cell-derived exosomes are capable of mediating intercellular communication between epithelium and mesenchyme during organogenesis of salivary gland, tooth, hair follicle, and kidney, shedding light on potential therapeutic benefits elicited by mesenchymal exosomes in nanomedicine. Representing the most extensively investigated multipotent stem cells, mesenchymal stem cells (MSCs) have been identified and extracted from a wide variety of tissues. Accordingly, exosomes derived from MSCs (MSC-Exos) can be easily accessed and manipulated as nanoparticles, giving rise to an entirely new therapeutic agents for nanomedicine. MSC-Exos have presently emerged as efficacious alternatives to MSCs for cell-free therapeutic strategies in disease contexts of ischemic heart disease, cutaneous wound healing and coronavirus disease 2019. In this review, we first present a critical analysis of research state of exosomes in terms of their biogenesis, molecular composition, isolation and characterization, then summarize current understanding of developmental regulation mediated by mesenchymal cell-derived exosomes and reparative potential conferred by MSC-Exos, along with particular emphasis on the underlying mechanisms of action and commentary on the major outstanding issues faced with MSC-Exos.