Decreased estrogen levels are one of the main causes of lipid metabolism disorders and coronary heart disease in women after menopause. Exogenous estradiol benzoate is effective to some extent in alleviating lipid metabolism disorders caused by estrogen deficiency, but the role of gut microbes in the regulation process is not yet clear. The objective of this 45 days randomized trial was to investigate the effects of estradiol benzoate supplementation on lipid metabolism, gut microbiota and metabolites in ovariectomized (OVX) mice, and revealing the important role of gut microbes and metabolites in the regulation of lipid metabolism disorders. This study found that high doses of estradiol benzoate supplementation effectively attenuated fat accumulation in OVX mice and significantly altered the expression of genes enriched in hepatic cholesterol metabolism and unsaturated fatty acid metabolism pathways. Further screening of the gut for characteristic metabolites associated with improved lipid metabolism disorders revealed that estradiol benzoate supplementation influences major subsets of acylcarnitine metabolites, and ovariectomy significantly increased the abundance of characteristic microbes that were significantly negatively associated with acylcarnitine synthesis, including Lactobacillus and Eubacterium_ruminantium_group bacteria, while estradiol benzoate supplementation significantly increased the abundance of characteristic microbes that were significantly positively associated with acylcarnitine synthesis, including Ileibacterium and Bifidobacterium bacteria. The use of pseudo-sterile mice gut microbial deficiency greatly facilitates the synthesis of acylcarnitine due to estradiol benzoate supplementation and alleviates lipid metabolism disorders to a greater extent in OVX mice. Our findings established a role for gut microbes in the progression of estrogen deficiency-induced lipid metabolism disorders, and screened for key target bacteria that may have the potential to regulate acylcarnitine synthesis. These findings suggest a possible route for the use of microbe or acylcarnitine to regulate estrogen deficiency-induced disorders of lipid metabolism.