The phrase "internal clock" refers to a natural sense of time that your body has. It helps you know when it's time to eat, sleep, or wake up without needing to look at a clock or get reminders from others. Full definition
That was one sign that the scientists could reset the plant's internal clocks by shifting when it encountered light and when its world went dark. (sciencenewsforstudents.org)
After we have a big meal, especially around lunchtime, the body just naturally has its own internal clock which tells us that we should be falling asleep around that time. (businessinsider.com)
It encourages us to move away from noticing seasonal changes in the light and responding with our own internal clocks. (mixedgreensblog.com)