In 1917, solar astronomer George Ellery Hale convinced Millikan to begin spending several months each year at the Throop College of Technology, a small academic institution in Pasadena, California, that Hale wished to transform into a major center for scientific research and education. A few years later Throop College became the California Institute of Technology (Caltech), and Millikan left the University of Chicago to become Caltechs "chairman of the executive council" (effectively its president).  Millikan served in that position from 1921 to 1945.  At Caltech, most of his scientific research focused on the study of "cosmic rays" (a term he coined). In the 1930s he entered into a debate with Arthur Compton over whether cosmic rays were composed of high-energy photons (Millikans view) or charged particles (Comptons view).  Millikan thought his cosmic ray photons were the "birth cries" of new atoms continually being created to counteract entropy and prevent the heat death of the universe.  Compton was eventually proven right by the observation that cosmic rays are deflected by the Earths magnetic field (hence must be charged particles).
Millikan was Vice Chairman of the National Research Council during World War I. During that time, he helped to develop anti-submarine and meteorological devices. During his wartime service, an investigation by Inspector General William T. Wood determined that Millikan had attempted to steal another inventors design for a centrifugal gun in order to profit personally. Wood recommended termination of Millikans army commission, but a subsequent investigation by Frank McIntyre, the executive assistant to the army chief of staff, exonerated Millikan. He received the Chinese Order of Jade. After the War, Millikan contributed to the works of the League of Nations Committee on Intellectual Cooperation (from 1922, in replacement to George E. Hale, to 1931), with other prominent researchers (Marie Curie, Albert Einstein, Hendrik Lorentz, etc.). Millikan was a member of the organizing committee of the 1932 Los Angeles Olympics, and in his private life was an enthusiastic tennis player. He was married and had three sons, the eldest of whom, Clark B. Millikan, became a prominent aerodynamic engineer. Another son, Glenn, also a physicist, married the daughter (Clare) of George Leigh Mallory of "Because its there" Mount Everest fame. Glenn was killed in a climbing accident in Cumberland Mountains in 1947.
In the aftermath of the 1933 Long Beach earthquake, Millikan chaired the Joint Technical Committee on Earthquake Protection. They authored a report proposing means to minimize life and property loss in future earthquakes by advocating stricter building codes.
A religious man and the son of a minister, in his later life Millikan argued strongly for a complementary relationship between Christian faith and science. He dealt with this in his Terry Lectures at Yale in 1926–27, published as Evolution in Science and Religion. He was a Christian theist and proponent of theistic evolution. A more controversial belief of his was eugenics – he was one of the initial trustees of the Human Betterment Foundation and praised San Marino, California for being "the westernmost outpost of Nordic civilization ... [with] a population which is twice as Anglo-Saxon as that existing in New York, Chicago, or any of the great cities of this country." In 1936, Millikan advised the president of Duke University in the then-racial segregated southern United States against recruiting a female physicist and argued that it would be better to hire young men.
  On account of Millikans affiliation with the Human Betterment Foundation, in January 2021, the Caltech Board of Trustees authorized removal of Millikans name (and the names of five other historical figures affiliated with the Foundation), from campus buildings.