<p>Subcellular lipid composition and transport substantially influence the physiological and pathological functions of both cells and organelles. However, lipid transport and turnover between organelles remain poorly understood due to a lack of methods for selectively labelling lipids in organelles. Here we develop a subcellular photocatalytic labelling strategy that enables organelle-selective lipid analysis by mass spectrometry and the quantitative profiling of lipid transport between organelles. We use this approach to quantitatively characterize fatty-acyl-dependent transport of phosphatidylethanolamine and phosphatidylserine lipids between the endoplasmic reticulum and mitochondria, the nucleus or lysosomes. Further experiments revealed the relative contributions of various biosynthesis pathways to the phosphatidylethanolamine and phosphatidylserine lipid compositions in the mitochondria, nucleus and lysosomes. Lysosome-specific photocatalytic labelling revealed the impact of the mTOR kinase pathway on lysosomal lipid metabolism. Together, this subcellularly localized photocatalytic labelling of lipids quantitatively deciphers the subcellular lipid composition and transport, enhancing our understanding of lipid metabolism in living organisms.</p><p></p>