The human characters are hand-drawn. John Silver's mechanical arm and the robot B.E.N. are flat-rendered CGI. The ship was created using Disney's 'Deep Canvas' process. In some scenes, all 3 types of animation appear simultaneously.
When Jim and Dr. Doppler arrive at the space-port they get directions from two characters using a ladder. These are caricatures of the two directors: John Musker (at the top of the ladder) and Ron Clements (holding the bottom of the ladder).
The first Disney film in which the maquettes (small character reference sculptures) were not made entirely by hand, out of clay. Silver's cyborg parts were constructed out of plastic, using laser technology.
On the planet in BENs cave, Dr. Doppler says the phrase "Dangit Jim, I'm not a doctor. I mean I am but it's a doctorate it's not the same thing." This is a reference to the Star Trek series where the medical doctor, Bones, always says "Damnit Jim, I'm a doctor, not a ____!" to Captain Kirk.
Originally Disney wanted to co-produced the film with Italian animation studio Rainbow S.r.l. seeing how there was a Treasure Island in Space mini series made in Italy in 1987. But Rainbow back out of the deal due to they were busy at the time.
To enhance his 'bad boy' reputation, the producers added a dark 'mask' over his eyes and gave Jim a black jacket, which he wears in most scenes for the first half of the film. However, in the second half, he is no longer seen wearing the jacket and by the final scene, the 'mask' is gone.
The trivia items below may give away important plot points.
At the end of the film, Dr. Doppler and Captain Amelia (two aliens) got together and had children. A few lines cut from the film revealed that Dr. Doppler (the male alien) gave birth to the children. Disney ordered the lines cut because they thought males giving birth, even male aliens, was too risqué for a children's movie.
Jim's clothes become lighter as the film progresses, symbolizing his transformation from 'bad boy' to 'hero'. Near the beginning, he wears a black T-shirt. During his adventure towards and on Treasure Planet, he wears a tan shirt. In the final scene, he wears a white military uniform.
The song "Always Know Where You Are" was written by John Rzeznik, who also performed the song during the end credits. However, on the soundtrack album, the song was performed by the British boy band BBMak.