The present study was aimed at examining the role of hypothalamic neuropeptides genes expressions on body mass regulation under different photoperiods in Eothenomys miletus, body mass, food intake, serum leptin levels and hypothalamic neuropeptide neuropeptide Y (NPY), Agouti related peptide (AgRP), pro-opiomelanocortin (POMC), cocaine and amphetamine regulated transcript (CART) expressions were measured. The results showed that short photoperiod reduced body mass and body fat mass, and increased food intake. But serum leptin levels showed no significant differences between short photoperiod group and long photoperiod group, and serum leptin levels showed a positive correlation with body fat mass. Hypothalamic neuropeptide NPY, AgRP, POMC and CART expressions had no significant differences between two groups. Leptin was negatively correlated with NPY expression, but not correlated with CART, POMC and AgRP expressions. All of the results suggested that short photoperiod can reduce body mass, body fat mass, increased food intake. Leptin may play a regulation on body mass and energy metabolism by acting on hypothalamic neuropeptide of NPY expression under different photoperiods in E. miletus.