Napoleon, like Stalin, reallly tries his best to create a totalitarian regime on the farm. He wants complete control and achieves it through various strategies, like eliminating dissent, using fear to suppress and control his enemies, and controlling information, through his own style of propaganda.
Another similarity is that like Stalin, who concluded a non-aggression pact with Nazi Germany, Napoleon makes a deal to sell timber to the animals' sworn enemies, the humans. Like Stalin, Napoleon paid dearly for the mistake, as the humans gave him counterfeit money and launched an attack on the farm.
These two are very much the same. Perhaps the clearest connection is between Napoleon's relationship with Snowball and Stalin's with Trotsky. Stalin felt threatened by Trotsky and had him exiled. It's also important to remember that Stalin conducted purges of anyone who he saw as a threat (like how Napoleon has the dogs kill various animals).
One of the most memorable correlations between the allegorical character of Napoleon and the historical person of Stalin is the treatment of political enemies. In Russia, Stalin imprisoned or killed many of his political enemies. This campaign was known as Stalin's purges. In Animal Farm, Napoleon first has four pigs executed for treason. After this, other animals begin to confess to crimes that they apparently did not commit (this happened in Russia also) and are also executed.