The high protein and phospholipid content of yolk granules, which are naturally occurring lipoprotein complexes, coupled with a low cholesterol level. The development and utilization of yolk granules require a detailed investigation of their nutritional composition and characteristics. This study aimed to analyze the differences in nutrient composition among yolk granules from different poultry (chicken, duck, and quail) by evaluating nutrient content, microstructure, and physicochemical properties, accompanying lipidomics techniques. The fi ndings revealed that the water, total lipid, and ash contents of duck yolk granules (DYG) were signifi cantly lower than those of chicken yolk granules (CYG) and quail yolk granules (QYG), while the average particle size of DYG was significantly higher than that of CYG and QYG. A total of 1146 lipids molecules were identifi ed through lipidome analysis, with glycerophospholipids (520) being the most abundant lipid class. The contents of sphingolipids content were highest in CYG, while the contents of glycerophospholipids, glycerides and fatty acyls were higher in QYG. QYG possesses a greater ω-3 and ω-6 polyunsaturated fatty acids content. Furthermore, 34, 19, and 51 lipid biomarker candidates were identifi ed in CYG/DYG, CYG/QYG, and DYG/QYG, respectively. This study off ers valuable insights into the nutritional properties of yolk granules from diff erent poultry eggs.