Food-derived cholesterol-lowering peptides have the practical benefit of inhibiting lipid absorption and regulating systemic cholesterol homeostasis. This work aimed to explore the antihyperlipidemia function of milk casein-derived peptides Leu-Gln-Pro-Glu (LQPE), Val-Leu-Pro-Val-Pro-Gln (VLPVPQ), and Val-Ala-Pro-Phe-Pro-Glu (VAPFPE) and investigated whether the function of these peptides affected the gut microbiome. According to the experimental findings, lipid metabolism disorder in hyperlipidemia mice was improved to various degrees by all three peptides, which dramatically lowered the levels of low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG) in the serum and inhibited the buildup of lipids in the liver and the development of steatosis. VAPFPE was found to reduce intestinal cholesterol absorption and the formation of cholesterol esters by inhibiting hepatocyte nuclear factor 4α (HNF4α), niemann-pick C1-like 1 (NPC1L1), and acetyl coenzyme A acetyltransferase 2 (ACAT2) expression and increase intestinal cholesterol efflux through up-regulation of ATP-binding cassette transporter G8 (ABCG8). VAPFPE also maintained cholesterol homeostasis by up-regulating liver low-density lipoprotein receptor (LDL-R) expression. The 16S rRNA analysis revealed that all three peptides improve the gut microbial composition, and VAPFPE specifically encouraged a rise in the proportional abundance of Bifidobacterium. The results shed light on the potential applications of bioactive peptides as functional health foods for lowering cholesterol.