A dust speck is dislodged from its obscure place and sent adrift through the Jungle of Nool. At the same time, Horton the elephant (Jim Carrey), the jungle’s eccentric nature teacher, takes a dip in the pool. The dust speck floats past him in the air, and he hears a tiny yelp coming from it. Believing that an entire society of microscopic creatures are living on that speck, he places it atop of a clover. Horton finds out the speck harbors the city of Whoville and its inhabitants, the Whos, led by Mayor Ned McDodd (Steve Carell).
He has a wife, Sally (Amy Poehler), 96 daughters (whose names all begin with the letter H), and one teenage son named JoJo (Jesse McCartney). Despite being the oldest and next in line for the mayoral position, JoJo doesn’t want to be the next mayor, and because he’s so scared of disappointing his father, never speaks. Once Horton begins carrying the speck with him, the city starts experiencing strange phenomena (earthquakes and changes in the weather), and the Mayor finds his attempts to caution Whoville challenged by the Town Council, led by the opportunistic yet condescending Chairman (Dan Fogler).
After he makes contact with Horton, the Mayor finds out from Dr. Mary Lou LaRue (Isla Fisher) that Whoville will be destroyed if Horton does not find a ”safer, more stable home”. Horton resolves (with the help of his best friend Morton the mouse (Seth Rogen)) to place the speck atop Mt. Nool, the safest place in the jungle. The head of the jungle, the Sour Kangaroo (Carol Burnett), disbelieving Horton’s beliefs, and resenting him for overshadowing her authority attempts several times to demand that Horton give up the speck, but Horton ignores her demands. Also taking force toward Horton are the Wickersham Brothers, a group of monkeys who love making misery. Eventually, the Kangaroo enlists a vulture named Vlad Vladikoff (Will Arnett) to get rid of the speck by force.
Vlad manages to steal the clover away from Horton and drops it into a massive field of identical pink clovers, causing an apocalyptic tremor in Whoville. After unsuccessfully picking nearly 3,000,000 clovers, Horton eventually recovers the clover (exactly the 3,000,000th clover). The Kangaroo eventually finds out (thanks by Mrs. Quilligan (Jaime Pressly)) that Horton still has the speck, and decides to rally the jungle community into fighting Horton, saying that Horton’s goal will lead to anarchy. Upon cornering him, the Kangaroo offers Horton an escape from punishment by renouncing Whoville’s existence.
When Horton refuses, in spite of his heartfelt speech, the Kangaroo orders the animals to rope and cage him, and to have the speck and the Whos destroyed in a pot of boiling beezlenut oil. The Mayor enlists all of his people to make noise by shouting ”We are here!”, as well as playing a variety of instruments, so the animals may hear them, assisted by Jojo’s ”Symphonophone”, an invention which creates a huge musical contribution, but still fails to penetrate the surface of the speck.
As Horton lies beaten and captured, the Kangaroo easily takes the clover, and releases it. Meanwhile, JoJo grabs the horn used to project Horton’s voice, runs up the highest tower and screams ”YOPP!”, breaking through the sound barrier just seconds before the speck hits the oil.
The Kangaroo’s son, Rudy (Josh Flitter) grabs the clover and returns it to Horton. The animals finally hear the Whos and realize the truth and isolate the Kangaroo for (without knowing by herself) tricking them. While being praised for his integrity by his neighbors, Horton even forgives the devastated Kangaroo, and she befriends him with a makeshift umbrella for Whoville. Here, the people of Whoville and the animals of Nool gather in song and recite the chorus from ”Can’t Fight This Feeling”. The film ends with the narrator (Charles Osgood) revealing that the Jungle of Nool, or rather Earth, is just one speck, like Whoville, among numerous others, floating in outer space.