High somatic cell counts in milk caused by mastitis significantly influence the quality of milk and result in substantial annual economic loss. This study evaluated the beneficial effects of melatonin (MT) on milk somatic cell count (SCC) in cows. To examine the effects of melatonin on SCC, one hundred twenty cows were divided into four groups based on milk SCC. In each group, half of the cows were treated with melatonin (S.C.). Melatonin treatment significantly reduced milk SCC. To explore the potential mechanism, 20 cows with relatively high SCC were selected to evaluate the biochemical and immunological profiles of their blood after melatonin treatment. Treatment with MT significantly reduced SCC in milk, lowered serum cortisol concentrations and increased the levels of albumin, alanine transaminase and lactate dehydrogenase. Following treatment with MT, the concentration of IgG and IgM rose transiently then decreased significantly, similar to changes observed for white blood cells and lymphocytes. In conclusion, MT treatment improved the quality of milk by reducing SCC. This may be due to melatonin improving immune activity in cows.