The seed of fenugreek (FS) was traditionally used in diets and as a spice in India, as well as medicine in China. It had anti-diabetic and anti-hypolipidemic effects. According to the theory of traditional Chinese medicine, the effects of FS were enhanced after salt processing. But the enhanced effect of salt-processed fenugreek seed (SFS) on anti-hyperlipidemia was not yet fully understood. By UPLC-QTOF-MS analysis, five flavonoids and six saponins were tentatively identified in SFS. Salt processing increased the dissolution of polysaccharides and trigonelline. FS and SFS significantly improved the serum biochemical indexes, including total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C) of hyperlipidemic rats, promoted the excretion of TC and total bile acid (TBA), and downregulated aspartate aminotransferase (AST). According to the results of factor analysis, FS and SFS restored the severity of hyperlipidemia to a similar extent, and SFS enhanced the excretion of cholesterol more significantly. FS and SFS reduced the ratio of Firmicutes/Bacteroidetes (F/B), which was upregulated in HFD group. Additionally, SFS significantly increased the abundance of Ruminococcus_1, which was negatively correlated with blood lipid levels. Thus, to regulate gut microbiota and promote the excretion of cholesterol were the mechanisms of the effects of SFS on hyperlipidemia. The higher amounts of total polysaccharides and trigonelline in SFS than in FS led to their different effects.