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I am looking for an anime movie or series about a boy that travels with a girl on a submarine named Nautilus, some connection with Jules Verne novel.

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Could this be Nadia: The Secret of Blue Water (1990-1991)? It was a TV series, but the first couple of episodes were broadcast together as a feature-length.

Although there's been several animated adaptation of 20,000 Leagues Under the Sea, this is the only one that meets both parts of the description in terms of age and key protagonists

Set in an alternate universe 1889, the series centers on Nadia, a 14-year-old girl of unknown origins, and Jean, a young, warm-hearted French inventor. Early in the story, the two protagonists are chased by Grandis Granva, Sanson, and Hanson, a group of jewel thieves who pursue Nadia for the blue jeweled pendant she possesses. After being rescued by Captain Nemo and his submarine, the Nautilus, the jewel thieves and the young protagonists join forces and participate in the struggle against the Neo-Atlantean forces, who seek to dominate the world.

In the process, Nadia and Jean save the world from violent domination by the Neo-Atlantean forces led by Gargoyle, explore worldly mysteries and the powers of the blue pendant, uncover Nadia's hidden family ties, and ultimately discover the secret origins of Nadia.

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