Metabolism is a complex biochemical process in living organisms that involves different biomolecules and consists of various reaction steps. To understand the multi-step biochemical reactions involving various components, it’s essential to elucidate in-situ dynamics and the correlations between different types of biomolecules at subcellular resolution. In this context, we integrated deuterium-probed pico-second laser scanning stimulated Raman Scattering (DO-SRS), multiphoton fluorescence (MPF), and second harmonic generation (SHG) into a single microscopy system to study metabolic activities in cells, tissues, and animals during aging and diseases. We further developed this multimodal microscopy into a super-resolution multiplex imaging platform using the Adam-based Pointillism Deconvolution (A-PoD) algorithm. By combining it with heavy water or deuterated metabolites probing (glucose, amino acids, fatty acids, etc.), we directly visualized the metabolic changes of various  biomolecules in animal organs such as the brain, adipose tissue, liver, muscle, and ovaries during aging processes (Mouse and Drosophila). We quantitatively analyzed the turnover rates of proteins and lipids, lipid unsaturation rates, and optical redox ratios in situ at the subcellular organelle scale. We also studied the spatially correlated distributions of various metabolites using a custom-designed analysis method. One of our key findings revealed that lipid turnover decreases earlier in aged female Drosophila compared to males. Additionally, we observed that dietary restriction and downregulation of the insulin/IGF-1 signaling (IIS) pathway, both known to extend lifespan, significantly enhanced brain lipid turnover in aging flies. This platform empowers researchers to quantitatively image various molecular events in the same region of interest. It provides powerful tools for early-stage disease detection, prognosis, and treatment, as well as for a deeper mechanistic understanding of the fundamentals of aging and diseases.