Stem cell therapies have great promise for treatment of many debilitating diseases and damaged tissues. Clinical trials evaluating the safety of cell-based therapies are currently under way. Today's biomedical imaging technology allows for real-time, noninvasive monitoring of grafted stem cells including their distribution, migration, survival and differentiation. Magnetic resonance imaging (MRI) of nanoparticle-labeled cells being one of the most commonly used techniques. In order to track cells by MRI, the cells need to be labeled with exogenous magnetic nanoparticles, resulting in some unavoidable deficiencies restrict its wide clinical application. Metabolic profile takes an important role in understanding and diagnosing the diseases, identify the cell and tissues types, valuating the treatment effect and prognosis. MR spectroscopy (MRS) as an excellent tool is being most widely used to obtain the metabolic profile and biomarkers of cells in non-invasively, therefore, it might become a new and powerful technology to monitor the transplanted stem cells. Recent three years, some researches about the metabolic profiling and unique biomarker of the stem cells, such as neural stem cell (NSC), mesenchymal stem cell (MSC), glioma-initiating cells(GIC) and embryonic stem cell (ECS) have been reported, and demonstrated great application prospect. In this overview article, the objecitve is to review the current advances with regard metabolic profiles of stem cells, methods for biomarkers extraction and acquisition, challenges and developmental direction of stem cell MR spectroscopy (MRS) studies.