This movie took ten years to make, having had the longest production cycle of any movie in Disney's Experimental Era, after it went through production hell, though the production mainly started after the release of Hércules (1997).
When Jim's mother sits with him on his bed to read his book, on his bookshelf, there is a Stitch doll in an astronaut suit.
The human characters are hand-drawn. John Silver's cyborg leg, arm, eye and the robot B.E.N. are flat-rendered CGI. The ship was created using Disney's "Deep Canvas" process. In some scenes, all three types of animation appear simultaneously.
The name of the ship, "R.L.S. Legacy", is a reference to the book's ("Treasure Island") author, Robert Louis Stevenson.
When Jim and Dr. Doppler arrive at the space-port, they get directions from two characters using a ladder. These are caricatures of directors John Musker (at the top of the ladder) and Ron Clements (holding the bottom of the ladder).