It is not unusual for a puppy to cry, howl or bark when left alone. He has recently left the comfort of his litter mates and his mom, and needs to know somewhere is around.
Firstly you need to ascertain that he does not want to relieve himself, nor is frightened, hungry etc, just like with a baby. Spend quality time with your puppy when he is awake, giving him mental stimulation by playing with him shortly before you put him to bed. Puppies need lots of sleep, and if they are tired will just flake out as long as they are comfortable.
Leave him with some toys so he can amuse himself if he wakes up. Puppies cant always 'hold' themself all through the night, and if he is waking as he needs to go outside, you should praise him, and then play with him a while before he will go back to sleep.
Unfortunately in my experience, having a puppy can be as tiring as a newborn baby, but with patience you will have a loving lifelong companion.