The effects of the four heating intensities (hot-spring egg yolk, HEY; soft-boiled egg yolk, SEY; normal-boiled egg yolk, NEY; and over-boiled egg yolk, OEY) on lipidomes of boiled egg yolks were investigated. The results indicated that four heating intensities had no significant effect on the total abundance of lipids and lipid categories except for bile acids, lysophosphatidylinositol, and lysophosphatidylcholine. However, of all the 767 lipids quantified, the differential abundance of 190 lipids was screened among the egg yolk samples at four heating intensities. Soft-boiling and over-boiling altered the assembly structure of the lipoproteins through thermal denaturation and affected the binding of lipids and apoproteins, resulting in an increase in low-to-medium-abundance triglycerides. The decreased phospholipid and increased lysophospholipid and free fatty acid in HEY and SEY suggests potential hydrolysis of phospholipids under relatively low-intensity heating. Results provide new insights into the effect of heating on the lipid profiles of egg yolk and would support the public’s choice of cooking method for egg yolks.