Five-month-old captive Hulunbuir sheep (Baerhu and short-fat-tailed, n =10 for each) were selected to study the effect of important gene networks related to fat metabolism on fat distribution and fatty acid profile. The results showed that the relative mRNA expression of the fat mass and obesity associated (FTO) and methyltransferase 3 (METTL3) genes in longissimus dorsi and triceps brachii, the relative mRNA expression of the AMP-activated proteinkinase (AMPK) gene in triceps brachii, biceps femoris and subcutaneous fat, and the relative mRNA expression of the carnitine palmitate transferase (CPT1) gene in longissimus dorsi, subcutaneous fat and tail fat were significantly higher in Baerhu sheep than in short-fat-tailed sheep (P < 0.05), and the proportion of saturated fatty acids in longissimus dorsi and biceps femoris, the proportion of polyunsaturated fatty acids in subcutaneous and tail fat, and the proportion of monounsaturated fatty acids in tail fat of Baerhu sheep were significantly higher than those in short-fat-tailed sheep (P < 0.05). The relative mRNA expression of the acetyl-CoA carboxylase (ACC) gene in muscle, and FTO, METTL3, PPARγ (peroxisome proliferators-activated receptor γ) and ACC in subcutaneous fat, the content and mass of intramuscular fat, total carcass fat mass, carcass fat percentage, the proportion of polyunsaturated fatty acids in longissimus dorsi and the proportion of saturated fatty acids in tail fat were significantly lower in Baerhu sheep than in short-fat-tailed sheep (P < 0.05). In conclusion, the differential expression of this gene network can affect fat metabolism and energy metabolism of different strains of Hulunbuir sheep to a certain extent and consequently fat distribution and fatty acid profile.