Lactobacillus　plantarumFZU3013,　a　probiotic　previously　isolated　from　the　traditional　brewing　process　ofHongqurice　wine,　may　have　the　beneficial　effect　of　improving　the　disorders　of　lipid　metabolism.　This　study　aimed　to　investigate　the　role　ofL.　plantarumFZU3013　in　improving　non-alcoholic　fatty　liver　(NAFL)　associated　with　hyperlipidemia　in　mice　fed　a　high-fat　diet.　The　results　indicated　thatL.　plantarumFZU3013　intervention　significantly　reduced　the　HFD-induced　body　weight　gain　and　the　abnormal　levels　of　serum　total　triglycerides　(TG),　total　cholesterol　(TC)　and　low-density　lipoprotein　(LDL-C),　and　inhibited　the　excessive　accumulation　of　liver　lipids.　In　addition,L.　plantarumFZU3013　also　promoted　the　excretion　of　bile　acids　through　feces.　Metagenomic　and　multivariate　statistical　analysis　revealed　thatL.　plantarumFZU3013　made　significant　structural　changes　in　the　intestinal　microbiome　of　the　mice　fed　with　HFD,　in　particular　by　modulating　the　relative　abundance　of　some　function　related　microbial　phylotypes.　Furthermore,　ultra-performance　liquid　chromatography　with　quadruple-time　of　flight　mass　spectrometry　(UPLC-QTOF/MS)-based　liver　metabolomics　demonstrated　thatL.　plantarumFZU3013　had　a　significant　regulatory　effect　on　the　composition　of　liver　metabolites　in　hyperlipidemic　mice,　especially　on　the　levels　of　some　important　biomarkers　involved　in　the　pathways　of　glycerophospholipid　metabolism,　fatty　acid　degradation,　fatty　acid　elongation,　glycerolipid　metabolism,　primary　bile　acid　biosynthesis,　arachidonic　acid　metabolism,etc.　Moreover,L.　plantarumFZU3013　regulated　the　mRNA　expression　levels　of　the　genes　responsible　for　liver　lipid　and　cholesterol　metabolism.L.　plantarumFZU3013　intervention　increased　the　hepatic　mRNA　levels　of　cholesterol　7　alpha-hydroxylase　(CYP7A1)　and　the　bile　salt　export　pump　(BSEP),　suggesting　enhanced　bile　acid　synthesis　and　excretion　from　the　liver.　These　findings　present　new　evidence　supporting　thatL.　plantarumFZU3013　has　the　potential　to　improve　lipid　metabolism　disorders　through　modulating　specific　intestinal　microbial　phylotypes　and　regulating　hepatic　lipid　metabolism　related　genes,　therefore　it　could　be　used　as　a　potential　functional　food　for　the　prevention　of　NAFL　and　hyperlipidemia.