Dedicated to digging into the game's lore. Bring your thinking caps.
It's one of those mysteries that has no real answer. The most likely answer is that it's from some kind of dragon considering the location or perhaps it belongs to a more powerful form of giant that was wiped out amidst the war with the dragons. Sadly it's never been referenced again and there's no strong theory on the skull.
I always found it too humanoid to consider it to be from a dragon, so my bet would be that it's from a giant. Granted, it would be from a particularly large and bestial variety of giant but considering how varied in size and morphology giants are in the Dark Souls games it's not exactly outside the realm of possibility.