An expression used to indicate the boss or someone otherwise in charge.

I don't see the point in calling someone more powerful than you a large dairy product... It just doesn't seem safe.

More colloquially, one might say The Big Kahuna instead.

The Big Cheese is also the main bad guy in Samurai Pizza Cats. He's a rat in the English version, and a fox in the Japanese. He also happens to be a transvestite.