Eep is a cave girl whose family is part of the classification homo erectus living in the harsh environment of the stone age with her overprotective father Grug, her kind mother Ugga, her grandmother Gran and her younger siblings Thunk and Sandy. The only family around after their neighbors met unfortunate ends, Eep lives a sheltered life protected by her father until one night she sees a light outside of the cave. Defying Grug's rule about going out after dark she follows it and meets a neanderthal boy, an inventive idealist named Guy and his pet sloth Belt who introduces Eep to fire and explains that he is escaping what he calls "The End" saying that a great cataclysm is coming that could destroy Eep and her family. She refuses to go with him, but he gives her a shell to use as a horn if she needed him. Grug, looking for Eep eventually finds her and grounds her for breaking the rules. On their way back to the cave, a tremendous earthquake causes its destruction, revealing a tropical wilderness behind it. They are forced to escape into it when a predator attacks them, and Grug seeks out to find the family a new cave to live in.

Upon encountering a feline "Macawnivore" dubbed "Chunky the Death Cat" by Gran, and pirahna-birds that send even him running, Eep calls for help with a horn like the shell Guy gave her. He comes and saves them by using a torch to dissuade the birds from attacking them. After a chaotic first encounter with fire, Eep's family realizes Guy's value at their survival and Grug bottles him to guide them toward the mountain he is seeking refuge at. After another of Grug's morale-lowering stories reflecting the day's events, Guy tells his own story of a safe paradise dubbed "Tomorrow". After introducing the family to shoes to get over rough terrain, Grug begins to get jealous of Guy's inventions and ideas, and when they become separated in a labyrinth of tunnels, the family excluding Grug find their own means of escaping. After his family stays in a treetop home of Guy's Grug tries to come up with several of his own ideas, such as a rug dubbed because it rhymes with Grug, sunglasses made from planks of wood. But each of these ideas fail, embarrassing Grug even further as his family decides to go with Guy to Tomorrow.

At the mountain, Grug attacks Guy when the others refuse to join him in a cave where he wants to settle. The tussle gets the two of them caught in a tar pit and Guy reveals his family died in one. Grug realizes his mistakes and the two make amends before tricking Chunky into freeing them by pretending to be a female Macawnivore in distress. Fleeing to the peak of the mountain, they are cut off from "Tomorrow" by an explosion, but Grug decides that his family is safer following the sun and throws them across, sharing a brief invention he calls a "hug" with Eep. Cut off from his family from the destruction, Grug seeks shelter in a cave and encounters Chunky who cuddles up to Grug for protection. Grug gets his first good idea and fashions an airship out of a skeleton and using the pirahna-birds as a means to fly across the chasm with Thunk's dog-crocodile Douglas, and several animals they'd encountered in their journey. Reuniting with his family and narrowly avoiding destruction they share a hug together and Grug gains a new perspective on life and stops being so overprotective.

Later, the Croods now live on the land and have settled on a vast beach where every day they can follow the light to "Tomorrow."