As a superb tool to visualize and study the spatial-temporal distribution of chemicals, Raman microscopy has made big impacts to many disciplines of science. While the label-free imaging has been the prevailing strategy in Raman microscopy, recent development and applications of vibrational/Raman tags, particularly when coupled with stimulated Raman Scattering (SRS) microscopy, have generated intense excitement in biomedical imaging. SRS imaging of vibrational tags has enabled researchers to study a wide range of small biomolecules with high specificity, sensitivity and multiplex capability, at single live cell level, tissue level or even in vivo. As reviewed in the article, this platform has facilitated imaging distribution and dynamics of small molecules such as glucose, lipids, amino acids, nucleic acids, and drugs that are otherwise difficult to do with other means. As both the vibrational tags and Raman instrumental development progress rapidly and synergistically, we anticipate that the technique will shed light onto an even broader spectrum of biomedical problems.