The meat quality of sheep and goats differs even within the same age, gender, and farming systems. Intramuscular fat (IMF) content is an important factor affecting the quality of livestock meat because it affects muscle color, tenderness, juiciness, water-holding capacity, and flavor. This study evaluates the differences in IMF deposition characteristics between Longdong cashmere goats and Tan sheep, and also explores the correlations between these variations and the gut microbiota. The results revealed that the IMF contents in shoulder and rump meat, as well as the blood lipid levels, of Longdong cashmere goats were higher than those of Tan sheep ( < 0.05). The content of fatty acid synthase (FAS) in the duodenum of the goats was lower, but the content of hormone-sensitive lipase (HSL) in both the pancreas and duodenum was greater ( < 0.05). The Chao1 and β diversity showed differences between the two breeds, observed not only in the abomasum but also in the colon. The specific microbiota identified from the goats were involved in the lipid metabolism pathway. The concentrations of acetic acid and propionic acid in the colonic and abomasal chyme were decreased in the goats when compared to the sheep ( < 0.05). The contents of FAS in the colonic chyme of the goats were significantly lower, while HSL in the abomasal chyme was significantly higher than that of the sheep. The correlation analysis of IMF deposition with gut microbiota showed that and in the abomasum, as well as , , and in the colon, were positively correlated with the IMF content in shoulder meat and the level of LDL (except for ), but negatively associated with the content of propionic acid (|r| > 0.45, < 0.05). This preliminary study has demonstrated that some specific bacteria in the abomasum and colon were associated with IMF deposition, while also providing an indicative reference range for further investigation into the effects of microbes on IMF deposition.