Ensign Nellie Forbush, a young American nurse stationed on a South Pacific island during World War II, has met and fallen in love with Emile de Becque, a middle-aged French plantation owner. Nellie, promising to think about the future of their relationship, rushes back to the hospital for her shift.

Meanwhile on the beach, Luther Billis and the American sailors lament about the shortage of available women (since Navy nurses are commissioned officers and off-limits to enlisted men). A feisty native nicknamed Bloody Mary flirts with the sailors and joins in their fun.

When U.S. Marine Lieutenant Joseph Cable arrives on the island, Bloody Mary tries to persuade him to visit Bali Ha’i which only officers can go to, and Billis offers to help him get a boat. Cable declines and reports to the island’s commanding officers, Capt. George Brackett and Commander William Harbison.

Cable has been assigned to a dangerous spy mission to another nearby island, now held by the Japanese. The military plans to ask Emile to accompany him because he used to live there. They ask for Nellie’s help in learning more about him, and she realizes she doesn’t know him well and decides to end the relationship with him.

However, before she has the chance to break things off, Emile reveals why he had to leave France: a story about a bully he stood up to and accidently killed in France long ago. He also expresses his love for her and asks her to marry him, and she realizes how much she loves him in return.

Emile declines to accompany Cable on the spy mission because of his hopes for a new life with Nellie. Thus, Commander Harbison tells Cable to go on leave until the mission can take place; and Cable, Billis, and Bloody Mary go to Bali Ha’i where Bloody Mary introduces Cable to her daughter, Liat. She and Cable are instantly attracted.

Meanwhile, Emile introduces Ngana and Jerome to her, and she is shocked when she realizes they are his children by his first wife, a dark-skinned Polynesian women. Nellie cannot overcome her racial prejudice and leaves.

On Thanksgiving Day, the GIs and nurses perform in a revue called “Thanksgiving Follies” that Nellie has helped put together. During the show, Cable leaves to see Liat. Now Bloody Mary pushes Cable to marry Liat and live a carefree life on the island. He is tempted but ultimately refuses, and Bloody Mary angrily drags Liat away.

After the show, Emile approaches Nellie and asks her to reconsider marrying him, but she still cannot let her prejudices go about his children’s Polynesian mother. Upset and confused, Emile asks Cable why she feels this way, and he says it is something that is taught at a young age. Emile mourns for the relationship that was almost his and agrees now to go with Cable on the spy mission behind enemy lines because now neither has much to lose.

The men get to the island undetected and are able to get communications back to headquarters about the enemy’s position. This information makes it possible for a major offensive, Operation Alligator, to start. War rages, including in the hearts of Cable and Nellie as they struggle with their prejudices and the changing world around them.