Life of Pi is divided into four sections. In the first section the main character Pi Patel, an adult Canadian, reminisces about his childhood in India. His father owns a zoo in Pondicherry. The livelihood provides the family with a relatively affluent lifestyle and some understanding of animal psychology. Pi describes how he acquired his full name, Piscine Molitor Patel, as a tribute to the swimming pool in France. After hearing schoolmates tease him by transforming the first name into "Pissing", he establishes the short form of his name as "Pi" when he starts secondary school. The name, he says, pays tribute to the irrational number which is the ratio of the circumference of a circle to its diameter. In describing his experiences Pi describes several other unusual situations involving proper names. Two visitors to the zoo, one a devout Muslim and one a committed atheist, bear identical names. A memorably ferocious tiger at the zoo bears the name Richard Parker as the result of a clerical error in which human and animal names were reversed.[9]

Pi is raised a Hindu who practices vegetarianism. As a fourteen-year-old he investigates Christianity and Islam and decides to become an adherent of all three religions, saying he "just wants to love God."[10][11] He tries to understand God through the lens of each religion and comes to recognize benefits in each one.

Shifting government policies lead to a decision by Pi's father to sell the zoo and emigrate with his wife and two sons to Canada. The second part of the novel begins with Pi's family aboard the Tsimtsum, the Japanese freighter that is transporting animals from their zoo to North America. A few days out of port from Manila, the ship encounters a storm and sinks. Pi manages to escape in a small lifeboat, only to learn that the boat also holds a spotted hyena, an injured Grant's zebra, and an orangutan. To Pi's distress, the hyena soon kills the zebra and then the orangutan. At this point Pi learns that a 450-pound Bengal tiger has been hiding under the boat's tarpaulin: Richard Parker, who had boarded the lifeboat with ambivalent assistance from Pi himself. The tiger kills and eats the hyena.

Frightened, Pi constructs a small raft out of rescue flotation devices, tethers it to the stern of the boat and retreats to it. He begins conditioning Richard Parker to take a submissive role by using food as a positive reinforcer and seasickness as a punishment mechanism while using a whistle for signals. Pi asserts himself as the alpha animal and is eventually able to share the boat with Richard Parker.

Pi recounts various events while adrift in the Pacific Ocean. At his lowest point, exposure renders him blind, feeble and unable to catch fish. In a state of delirium he talks with a marine "echo" that he eventually identifies as Richard Parker finally speaking up, then identifies as another survivor on another lifeboat who is also blinded by exposure and dying. They share dreams of food. The other voice speaks with a French accent and prefers meat to the vegetarian fare Pi longs for. Pi welcomes this "brother" aboard his boat. The other person moves to attack and eat Pi but is instead devoured by Richard Parker, who springs out at him from under the tarpaulin. Later, his sight restored, Pi's boat comes ashore on a floating island network of algae and inhabited by meerkats. Pi gains strength but his discovery that the island's plant life is carnivorous forces him to return to the boat. Two hundred and twenty-seven days after the ship's sinking, the lifeboat washes onto a beach in Mexico. Richard Parker disappears into the nearby jungle without a glance back.

The third part of the novel describes a conversation between Pi and two officials from the Japanese Ministry of Transport who are conducting an inquiry into the shipwreck. They meet him at the hospital in Mexico where he is recovering. Pi tells them his tale but the officials reject it as unbelievable. Pi then offers