From Pixelmon Wiki
An Ultra Ball has a catch rate of 2× the normal Poké Ball's catch rate. It is more effective than a Great Ball. It can be obtained by crafting it, buying from a shopkeeper, or as a tier 1 special drop,
Crafting
Ultra Balls are crafted similarly to other Poké Balls.
Ultra Ball is also used to craft a Good Rod.
Trivia
Ultra Balls used to be crafted differently. This recipe no longer works.