Mesenchymal stem cells (MSCs), the most well-studied cell type in the field of stem cell therapy, have multi-lineage differentiation and self-renewal potential. MSC-based therapies have been used to treat diverse diseases because of their ability to potently repair tissue and locally restore function. An increasing body of evidence demonstrates that paracrine function is central to the effects of MSC-based therapy. Growth factors, cytokines, chemokines, extracellular matrix components, and extracellular vehicles all contribute to the beneficial effects of MSCs on tissue regeneration and repair. The paracrine substances secreted by MSCs change depending on the tissue microenvironment and biological behavior. In this review, we discuss the bioactive substances secreted by MSCs depending on the microenvironment and biological behavior and their regulatory mechanisms, which explain their potential to treat human diseases, to provide new ideas for further research and clinical cell-free therapy.