Lipid metabolism disorder has become an important hidden danger threatening human health, and various supplements to treat lipid metabolism disorder have been studied. Our previous studies have shown that DHA-enriched phospholipids from large yellow croaker (Larimichthys Crocea) roe (LYCRPLs) have lipid-regulating effects. To better explain the effect of LYCRPLs on lipid regulation in rats, the fecal metabolites of rats were analyzed from the level of metabolomics in this study, and GC/MS metabolomics measurements were performed to figure out the effect of LYCRPLs on fecal metabolites in rats. Compared with the control (K) group, 101 metabolites were identified in the model (M) group. There were 54, 47, and 57 metabolites in the low-dose (GA), medium-dose (GB), and high-dose (GC) groups that were significantly different from that of group M, respectively. Eighteen potential biomarkers closely related to lipid metabolism were screened after intervention with different doses of LYCRPLs on rats, which were classified into several metabolic pathways in rats, including pyrimidine metabolism, the citric acid cycle (TCA cycle), the metabolism of L-cysteine, carnitine synthesis, pantothenate and CoA biosynthesis, glycolysis, and bile secretion. L-cysteine was speculated to be a useful biomarker of LYCRPLs acting on rat fecal metabolites. Our findings indicated that LYCRPLs may regulate lipid metabolism disorders in SD rats by activating these metabolic pathways.