Hi Tabarak. The reason is simple. The regulation of the suprachiasmatic nucleus (SCN), stemming from the hypothalamus, is responsible (alongside a few other factors). Cortisol and melatonin peak at different times, and the SCN ensures no conflicting signals to the best of its ability. Cortisol peaks when we wake up, while melatonin peaks in the night. They have opposite circadian rhythms so to speak. Inhibitory wise, melatonin has been shown to blunt adrenal cortisol output even when the adrenal is stimulated, assisting in keeping it lower on top of the SCN's base regulation. It inhibits the ACTH-stimulated cortisol output. Further more, it is directly associated with light. Melatonin peaks during the darker times of day, while cortisol peaks during brighter times, as I touched upon. Cortisol won't happen the same at night due to inhibitory suppression, and melatonin won't happen during the day because of the light. This ensures a direct correlatory balance between melatonin and cortisol. Hope this answered your question. Best of luck.