A major difference between the United Nations and the African Union is that the United Nations have global influence, while the African Union has influence only on the African continent.
The United Nations are the biggest and most influential organization on the planet. Most of the countries in the world are members of it. It has its own military, laws that have to be practiced by all country members, and pretty much dictates the global politics and economy.
The African Union, on the other hand, only has members form the African continent and its influence is also only in Africa. It has to be said though that the influence that this organization has is not really big, and it doesn't enjoy big authority. Also, it has shown that it has a long way to go in order to be strong organization as it has failed terribly in most of its missions and actions.