The development of animal husbandry is closely related to the meat quality of small ruminants. Intestinal metabolites and the muscle fiber types of lambs are important factors that affect their meat quality, but few studies have examined the regulation of the "intestinal muscle axis" by probiotics. In this study, 12 Sunit lambs were divided into a control group (C) and a probiotics group (P). The gene expressions of the myosin heavy chain, metabolic enzyme activity, and short-chain fatty acids in the intestines were analyzed using gas chromatography-mass spectrometry (GC-MS) and quantitative real-time PCR. The results showed that levels of propionic acid and butyric acid in the intestines of group P were significantly higher than in group C (p < 0.05). In addition, probiotics increased the number and area ratio of type I muscle fibers. They also increased the mRNA expression of MyHC IIA and the activity of malate dehydrogenase (MDH) and succinate dehydrogenase (SDH). Propionic acid was negatively correlated with the number ratio of type IIB muscle fibers. Butyric acid was found to be significantly positively correlated with the number ratio of type IIA muscle fibers. Cooking loss, pH_24h, and shear force decreased significantly in group P. In conclusion, intestinal metabolites (SCFAs) altered the activity of oxidative-myofibril-metabolizing enzymes and the expression of myosin heavy-chain type IIA, reduced the meat shear values, and improved meat tenderness. This study provides a new basis for improving the production and meat quality of small ruminants.