This is Kaena: The Prophecy (2003).
The film begins with an alien ship crash landing on a desert planet.
The alien survivors, known as Vecarians, are quickly killed by the
planet's predatory native inhabitants, the Selenites. The ship's core,
Vecanoi, survives, and from it sprouts Axis, a massive tree reaching
up into space.
600 years later, a race of human-like tree-dwellers have evolved
living in the branches of Axis. One of them, a young girl named Kaena
(voiced by Kirsten Dunst), is an adventurous daydreamer who longs to
explore the world beyond the confines of her village. Kaena's
inquisitiveness is opposed as heresy by the village elder, who
commands his people to stay productive and toil for the villager's
gods (who are, unbeknownst to them, the Selenites living in the planet