Yeah, the Dragon can be a real pain. I think him and that flying demon with the armor in Northwall Act 1 are the hardest bosses in the game, excluding the final boss.
Are you using spell scrolls against him? It's been a while since I fought him, but I would think spell scrolls would be very useful since you are invincible while you are using it.
The good news about the Dragon is, since he is not a major boss, you don't have to fight him or the blue flying demon again once you get to Deathheim. You do have to fight that S.O.B. minotaur again though.
*Did anyone else notice Enix do the "refight all the bosses over again before the last boss" deal on the SNES a lot besides me?
Really, you have to do it in ActRaiser I, II, Illusion of Gaia and Skyblazer. At least I think Skyblazer is an Enix game.