How old is he?
He would rather be in a small crate next to you then a large pen all alone.
I know the feeling because when I first brought my pup home she would cry every hour on the hour just for a cuddle most of the time. I think its because they have never been alone before, from the second they were born they had mom and litter mates so when they wake up in the night and they are alone its scary for them.
I started to put Poppy in a play pen downstairs and I would sleep on the sofa where she could see me and she stopped crying in the night.
I did that for a few weeks then moved her back into her crate in my room, at the bottom of my bed. She cant see me but she will know I am there.
I think after a while they learn that they arn't alone and that when they wake up in the morning you will still be there, they are just babies and need time to learn.
Poppy is 7 months old and still sleeps in her crate in my room, I think she will always sleep in my room.
Good luck.