Dietary phosphatidylcholine (PC) is an ideal source of bioactive lipids showing efficacy to alleviate non-alcoholic fatty liver disease (NAFLD). In this study, the lipidomic profiles of nonalcoholic steatosis in mice and HepG2 cells treated with PC isolated from eggs (EPC) and soybean (SPC) were evaluated. EPC and SPC could significantly ameliorate fatty liver disease by down-regulating triglyceride (TG) and diglyceride (DG) levels. Remarkably, EPC exhibited better performance in regulating the hepatic lipid profile leading to decreased PC and TG, ceramides, phosphatidylethanolamine and phosphatidylserine levels. A total of 117 and 20 lipid biomarkers in liver and HepG2 cells involved in glycerophospholipid metabolism were screened out, respectively. The regulatory mechanism of EPC may be attributed to a decrease in the expression of ACACA and SREBP-1c. EPC, via suppressing lipogenic gene expression, which was superior to that of SPC in alleviating nonalcoholic steatosis. Overall, EPC and SPC attenuated HFD-induced NAFLD by improving the hepatic lipid profile. The more significant effect observed with EPC may be attributed to its modulation of glycerophospholipid metabolism.