Can you say "In the night" to mean during the night, but in a more natural and informal way? for instance, I wake up several times in the night just to use the bathroom.
I find in the night is quite frequently used in conversation, and even in writing. Here are some examples of it being used correctly
I woke up in the night to use the restroom.
I heard a coyote howling in the night.
The tree branches scratched my windows in the night and woke me up.
These examples provide a good idea of context for using in the night. It should be noted that in the night can not usually be used plurally, such as saying
I woke up in the nights because of a sound.
But you could get away with saying:
I woke up every night in the nights that preceeded my death.
But it's probably more smooth to write that:
The difference between 50 minutes and 35 minutes may not seem like much. But it means that, in the nights after the full Harvest Moon, you’ll see the moon ascending in the east relatively soon after sunset.
So I would say it's best to stick with using that phrase in singular form.
Though I hear it frequently used, some other answers say that during the night is better. I tend to use them interchangeably, and find neither to be more correct than the other.
It is not common. Here we would say
1) "I wake up several times a night just to use the bathroom."
2) "I wake up several times during the night."
3) "I wake up several time in the middle of the night.