Dietary supplementation with omega-3 polyunsaturated fatty acids (n-3 PUFAs) for laying hens enriches eggs with these essential fatty acids. However, the enrichment patterns and changes to intact lipids in egg yolk have not been sufficiently revealed. Herein, egg yolk lipids from hens fed with diets supplemented with flaxseed, Schizochytrium sp. residue, or their mixture were comprehensively analyzed using ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). A total of 335 individual lipid species covering 23 (sub)classes were identified and quantified. Distinct n-3 PUFA-lipid profiles were revealed among different groups. Dietary α-linolenic acid (ALA) was mainly deposited in the TAG fraction, whereas synthesized or preformed docosahexaenoic acid (DHA) predominantly existed in the glycerophospholipid form. Furthermore, different lipid species were identified and related lipid pathways after dietary supplementation were analyzed. Collectively, these findings provide us with new knowledge for production, nutritional evaluation, authentication, and application of n-3 PUFA-enriched eggs.