Mothra stars in the movie because a poll showed that she was the most popular monster among women, who made up the bulk of movie-going audiences. The lighter tone, the family-oriented romance story, and child main character were all put into the movie to appeal more to a crowd of women and children. These factors contributed to the film's box office success, becoming the most successful Heisei film and bring in profits not seen since the the golden age of the early 1960s.
During a trip to Japan, director Tim Burton was on the film-set during the first day of special effects filming.
Ishirô Honda, who directed the original Godzilla, visited the set shortly before passing away. During the Heisei series, Toho had offered Honda to return as director, but he declined each time. According to Honda, while he didn't have any positive or negative feelings on them, he felt the Heisei films lacked imagination, stating "If they continue to make Godzilla films like they are now, where it simply comes to Japan, I feel that the meaning of Godzilla will be greatly diminished."
In the movie, the characters don't react with much of a surprise to the appearance of Mothra, her fairies and Battra. When asked why this is, director Takao Okawara just said "It's a monster movie, so of course it has monsters in it."
This film's origin went back to 1990 with the concept Mothra Vs. Bagan. The film would include battles all across Asia in places like Shanghai and Bangkok. However, when Gojira tai Biorante (1989) did not turn out to be the hit Toho wanted, they felt that it was because of an unfamiliar monster was used and this project was put on hold to give Godzilla another shot with Gojira tai Kingu Gidora (1991).