Your puppy's interest in litter and the stinky stuff it covers likely revolves around normal puppy behavior, although it can turn into a compulsive condition. Preventing him access to the box is key to stopping the habit.
Coprophagia is the act of eating feces. Two types of coprophagia exist: non-compulsive and compulsive. Most puppies fit into the non-compulsive category. Your youngster most likely enjoys sticking his furry head inside the cat litter box for a nasty treat for the same reason that he runs off with your shoes, eats toilet paper and engages in one of his other bratty little behaviors. They're fun. It's normal puppyhood doings. Puppies are curious and feisty, and they become bored quickly. Those qualities that define puppies often result in the little ones getting into things they shouldn't -- like cat litter. If when your pup passes into adolescence and adulthood and is still drawn to the cat box like metal to a magnet, you may have a case of compulsive coprophagia on your hands.
The simplest way to prevent your puppy from rummaging through your cat's litter box is to block his access to it. Baby gates, stools, chairs and laundry baskets can thwart a puppy's attempts to get inside the litter box. Placing the box knee-high or higher may work. If those options don't solve the problem or aren't feasible, consider a top-entry litter box, which has a hole at the top so ideally only your cat can get inside. Be aware, though, that changing your kitty's litter box arrangement can result in an upset feline who may choose to relieve herself elsewhere.