Understanding the dynamics of metabolism in a multicellular organism is essential to unraveling the mechanistic basis of many biological processes. It is the synthesis, transformation and degradation of biomolecules (the definition of metabolism) that carry out the genetic blueprint, which cannot be imaged in vivo by using traditional methods. In the present work, we developed a new method that combines D2O probing and Stimulated Raman Scattering microscopy (DO-SRS) to visualize metabolic dynamics in live animals. The enzymatic incorporation of D2O-derived deuterium (D) into biomolecules will generate carbon-deuterium (C-D) bonds in macromolecules. Within the broad vibrational spectra of C-D bonds, we discover lipid-, protein-, and DNA-specific Raman shifts and develop spectral unmixing methods to obtain C-D signals with macromolecular selectivity. We obtained new biological insights in several studies such as the spatial dependence of lipogenic activities of sebaceous glands, specific myelination timing of the developing mouse brain, differential protein and lipid metabolism in germline development of C. elegans as well as its aging process, the spatial constrain for the distribution of newly synthesized yolk proteins in aged C. elegans, the prevalence of protein biosynthesis and the lack of lipogenesis in zebrafish embryos, and intratumoral metabolic heterogeneity. In summary, we demonstrated that our current DO-SRS method is better than other deuterium-labeled carbon substrate in monitoring and imaging metabolic activities. This technique can track specifically de novo lipogenesis, image in vivo protein biosynthesis without tissue bias, and can simultaneously image spatial temporal dynamics of lipid and protein.