Atherosclerosis (AS) is the leading cause of heart attacks, stroke, and peripheral vascular disease. Berberine (BBR), a botanical medicine, has diversified anti-atherosclerotic effects but with poor absorption. The aim of this study was to develop an effective BBR-entrapped nano-system for treating AS in high-fat diet (HFD)-fed
Apoe
(−/−)
mice, and also explore the possible underlying mechanisms involved. Three
d
-
α
-tocopherol polyethylene glycol (PEG) succinate (TPGS) analogues with different PEG chain lengths were synthesized to formulate BBR-entrapped micelles. HFD-fed
Apoe
(−/−)
mice were administered with optimized formula (BBR, 100 mg/kg/day) orally for 5 months. The artery plaque onset and related metabolic disorders were evaluated, and the underlying mechanisms were studied. Our data showed that, BT
1500
M increased BBR deposition in liver and adipose by 107.6% and 172.3%, respectively. In the
Apoe
(−/−)
mice, BT
1500
M ameliorated HFD-induced hyperlipidemia and lipid accumulation in liver and adipose. BT
1500
M also suppressed HFD-induced chronic inflammation as evidenced by the reduced liver and adipose levels of interleukin-6 (IL-6), tumor necrosis factor-
α
(TNF-
α
) and interleukin-1
β (
IL-1
β
); and decreased plasma level of TNF-
α
, IL-6, IL-1
β
, interferon-
γ (
IFN-
γ
), monocyte chemotactic protein (MCP), and macrophage inflammatory factor (MIP). The mechanism study showed that BT
1500
M changed
Ampk
and
Nf-κb
gene expression, and interrupted a crosstalk process between adipocytes and macrophages. Further investigation proved that BT
1500
M decreased endothelial lesion and subsequent macrophage activation, cytokines release, as well as cholesteryl ester gathering in the aortic arch, resulting in ameliorated artery plaque build-up. Our results provide a practical strategy for treating AS using a BBR-entrapped nano-system.