"You are the true master of death, because the true master does not seek to run away from Death. He accepts that he must die, and understands that there are far, far worse things in the living world than dying." (35.88)
Dumbledore explains the real meaning of "master of death" here – it doesn't mean that Harry commands Death, but rather that he's kind of on equal terms with it. Like the third brother in the story (his ancestor), he's willing to approach Death face-to-face when the time is right, and thus has a greater understanding of it… or, rather, has come to an understanding with it.