He is best known for the Hugo and Nebula Award winning novella "Enemy Mine", which was subsequently made into an identically titled movie and a novelization in collaboration with David Gerrold. The story tells of an encounter between a human and an alien soldier, whose races are in a state of war. They are marooned together in space and have to come to grips with the universal problem of facing and accepting xenophobia. A greatly expanded version of the original novella as well as two novels completing the trilogy, The Tomorrow Testament and The Last Enemy are gathered with additional materials into The Enemy Papers.

The original novella, in part, helped Longyear to win the John W. Campbell Award for best new writer for 1980. He is the only writer to win the Hugo, the Nebula, and the Campbell in the same year. (Contrast the other SF "triple crown" winner: William Gibson with the Hugo, Nebula, and Philip K. Dick Award in 1984.)

He also wrote the Circus World and Infinity Hold series, several stand-alone novels, numerous short stories, and two books for the Alien Nation novelisation series. His trilogy "Infinity Hold," "Kill All the Lawyers," and "Keep the Law," was released in 2002 in a single paperback volume titled Infinity Hold 3 by the Author's Guild in a Backinprint.com edition. His recent Jaggers & Shad mystery stories, featuring two detectives in the Artificial Beings Crimes Division (Devon Office)are set mostly in Exeter and the surrounding Devon countryside and villages. The first of the tales, "The Good Kill" won the Analog AnLab award for Best Novella in 2006 and "Murder In Parliament Street" won the same award for 2007.

The Circus World series chronicles the path taken by a space-going circus troupe whose spaceship crashes, marooning them on a deserted planet with no contact with the outside world.

The Infinity Hold series poses, then answers the question of what type of society would arise from a mob of violent convicts dumped on a new planet with no police or government.

Saint Mary Blue is a thoughtful novel about the course of treatment of a man who has substance abuse and mental health issues, which resident in a treatment facility. While a work of fiction, it very accurately depicts different types of patients and a variety of behaviors.

Stand-alone novels

1. Sea of Glass
2. The God Box
3. Naked Came the Robot (1988) ISBN 0-445-20755-8

Novelettes

1. Homecoming (Asimov's Science Fiction Oct 1979) (1980 Hugo nominee)
2. Savage Planet (1981 Hugo & Locus nominee)
3. Chimaera (1993 Locus nominee)
4. The Death Addict (1994 Locus nominee)
5. The Hangingstone Rat (2008 AnLab nominee)
6. The Purloined Labradoodle (2009 AnLab nominee)

Enemy Mine Series

1. Enemy Mine (Asimov's Science Fiction Sep 1979) (1980 Hugo, Nebula & Locus winner)
2. The Tomorrow Testament (1983)
3. The Last Enemy (1997)
4. Collected in The Enemy Papers with additional material (1998) ISBN 1-56865-949-0

Infinity Hold Series

1. Infinity Hold 1989
2. Infinity Hold\3 2002 (The complete IH trilogy: Infinity Hold, Kill All the Lawyers, and Keep the Law)

Circus World Series

1. Circus World (1980)
2. City of Baraboo (1980)
3. Elephant Song (1981)

Short story collections

1. Manifest Destiny (including "Enemy Mine" and others in the same future history)
2. It Came from Schenectady

Jaggers & Shad Mystery Series

1. "The Good Kill" Analog Magazine November, 2006
2. "The Hangingstone Rat" Analog Magazine October, 2007
3. "The Purloined Labradoodle" Analog Magazine January/February 2008
4. "Murder In Parliament Street" Analog Magazine November, 2007

Recovery works

1. The Monopoly Man Fantasy & Science Fiction, January 2009
2. Yesterday's Tomorrow: Recovery Meditations For Hard Cases Hazelden, 1997
3. Saint Mary Blue (Novel set in a treatment facility) SteelDragon Press, 1988

Writing Instruction

1. Science-Fiction Writer's Workshop-I
2. The Write Stuff Online Writing Seminar