Simon is the most spiritual of the boys on the island. He is filled with goodness and is often understood as the novel's Christ figure. He stands for conscience and morality.
Therefore, it is not surprising that he is able to communicate with the Lord of the Flies, the pig's head on a stick surrounded by buzzing flies. This pig's head symbolizes the evil that Jack has unleashed in himself and the others.
In a hallucinatory conversation Simon has with the pig's head, Simon intuits that, as the pig says, even he, Simon, has the Lord of the Flies's evil impulses residing in his soul. The Lord of the Flies says to him,
You knew, didn’t you? I'm part of you?
This is significant in making explicit an important theme of the novel: that the capacity for evil lies within the human psyche. It is not "out there" in a mythical "beast" but is part of the aggressive, atavistic, sadistic tendencies that all humans must learn to control to be part of civilization.
The Lord of the Flies makes clear that evil wants no part of a person like Simon. His conscience and decency only get in the way of the boys' unleashing their most atavistic impulses in order to have "fun." The head says to Simon,
You’re not wanted. Understand? We are going to have fun on this island. Understand?