This paper introduces a Spectrum and Polarization Optical Tomography (SPOT) technique for studying subcellular lipidomics in live cells using Nile Red staining. SPOT simultaneously resolves membrane morphology, polarity, and phase from three optical dimensions. The high-throughput optical properties reveal lipid heterogeneities across ten subcellular compartments at different developmental stages. Real-time monitoring of multi-organelle interactive activities during cell division reveals sophisticated lipid dynamics.