Ray Harryhausen has related the story of watching a cut of the film with composer Bernard Herrmann. In a sequence involving a giant bird, Herrmann told Harryhausen that he was going to score it with "Turkey in the Straw" (he was only kidding).
A real Brown crab was disemboweled, dismembered, cleaned and fitted with an internal armature for Ray Harryhausen's stop-motion animation of the giant crab. Additional live crabs were used for some of the "facial" close-ups, then later cooked for a crew dinner.
Although produced by different studios, it is obvious that the exterior design of the "Nautilus" submarine as seen in the film was heavily influenced by Harper Goff's "half crocodile/half shark" Nautilus design in Disney's 20000 Leagues Under the Sea, especially with respect to the sub's top spar and rounded "eye" windows. In the original Jules Verne novels of "20,000 Leagues Under the Sea" and "Mysterious Island", the Nautilus is described as being rather plain, basically a cigar-shaped steel tube with very little outside detailing.
One of the factors that led to the green-lighting of this project was the huge success of a film with a similar story, Swiss Family Robinson, that was made by Walt Disney.
Originally, there was going to be a scene featuring a man-eating plant, but it was never shot.
Producer Charles H. Schneer claimed that he chose this story after reading an article stating that Jules Verne's "Mysterious Island" was the most-looked-at book at public libraries.
The armature for the crab is covered with the shell of a real crab instead of the usual latex. Ray Harryhausen bought three crabs for the production, having one humanely killed by a museum employee as boiling it would have changed the color of the shell. The other two were used for close-ups of the crabs' mandibles, which would otherwise have required a huge amount of time to properly animate. These crabs subsequently served as a dinner entrée for Harryhausen and producer Charles H. Schneer.
The opening scenes at the Confederate prison camp were shot in England and the exteriors were shot at Shepperton Square.
The original concept for the film was that it was going to be shot as a straight survival story without the giant animals. However, the producers felt that concept was too boring and decided to include the giant monsters.
The scene with the giant bird was from the original draft of the script, which was to have had prehistoric monsters rather than giant oysters and crabs.
The scenes on the island were actually filmed on the coast of Spain.