Discouraged by his progress as an art student, Limón in 1930 began to study dance with Doris Humphrey and Charles Weidman; he became one of the leading dancers of their company in New York City until 1940. After World War II he established his own company, with Humphrey as artistic director. His first major work, The Moor's Pavane (1949; music by Henry Purcell), conveyed the jealousy, rage, and remorse of Shakespeare's Othello within the framework of a stately court dance. Much of Limón's choreography was developed from natural gesture and expressed, as he said, “human grandeur, dignity, and nobility” through themes drawn from history, literature, and religion. His dances were also characterized by well-defined structure and form. Other successful works include Missa Brevis (1958; music by Zoltán Kodály), which portrayed the sustaining faith of survivors of World War II bombings, and La Malinche (1949), based on a Mexican legend. Limón and Pauline Koner, guest artist with his company for several years, created many of the leading roles in his dances.

Limón's company was the first to be sponsored by the U.S. State Department's International Cultural Exchange Program, performing in South America in 1954; subsequently the company toured Europe, Central America, and the Far East, in addition to annual tours of the U.S. Limón has also danced and choreographed for the National Academy of Dance in Mexico. The José Limón Dance Company survived the death of its founder and continues to perform on both national and international scenes.