Obesity is generally defined as an excess of body fats and related to weight gain. The hypothalamic arcuate nucleus (ARC) is responsible for regulating peripheral signals that control food intake and energy balance. Uncoupling protein-1 (UCP-1) and UCP-2 are related-genes that adjust body weight. The aim of this study is to explore the effect of fat-1 gene on body weight. We found that the weight/length ratios of fat-1 transgenic mice were smaller than wild-type (WT) mice. We hypothesized that an increase in the levels of n-3 PUFAs might alter the expression of hypothalamic neuropeptide and lead to weight loss in fat-1 mice because fat-1 gene transforms n-6 polyunsaturated fatty acids (PUFAs) to n-3 PUFAs. Therefore, the appetite-regulating neuropeptides in the hypothalamic ARC, including neuropeptide Y (NPY), agouti-related peptides (AgRP), proopiomelanocortin (POMC), cocaine and amphetamine regulated transcript (CART), and ghrelin, were measured by Immunofluorescence. The mRNA levels of UCP-1 in brown adipose tissues and UCP-2 in white adipose tissues were measured by RT-PCR. The protein levels of UCP-2 in white adipose tissues also were measured by Western Blot. Compared with WT mice, the levels of CART, POMC and ghrelin increased, the levels of NPY and AgRP decreased, whereas the mRNA levels of UCP-1, UCP-2 increased, the protein levels of UCP-2 increased in fat-1 mice. The results indicated that the fat-1 gene or n-3 PUFAs participate in inhibition of body weight by regulating the expressions of appetite neuropeptide and uncoupling protein.