- "Exhalation: Stories" (2021)
- "New York 2140" (2021)
- "Rewilding Earth: A Personal Journey Through the Science and Politics of Conservation" (2019)
- "The Great Beyond" (2018)
- "The Gray Whales of Mexico: A Story of Science and Conservation" (2018)
- "All Our Wrongs Today: A Novel" (2017)
- "The Ministry of the Future: A Novel" (2020)
- "Singularity Rising: A Novel" (2018)
- "The Time Traveler's Wife" (2015)
- "The City and The City: A Novel" (2010)
- "Jack Glass: A Novel" (2009)
- "The Palace of Thorns: A Novel" (2008)
- "The Third Tiger: A Novel" (2005)
- "Into the Silent Land: Travels in a Post-Apocalyptic World" (2004)
- "The Chronological History of Conquest" (2002)
- "The Sparrow: A Novel" (2002)
- "Darwin's Children: A Novel" (2000)
- "Boneshaker: A Novel" (1999)
- "The Book of Strange New Things: A Novel" (2014)
- "In the Shadow of the Sun" (2001)
Short Stories Collections
- "Exhalation: Stories" (2021)
- "The Best American Science Fiction and Fantasy 2021" (Edited with John Joseph Adams) (2021)
- "A Song for a New Day" (2020)
- "The New Voices of Science Fiction" (Edited with Ken Liu and George R. R. Martin) (2018)
- "The Big Idea: 20 Short Stories from 20 Big Minds" (2018)
- "The Best American Science Fiction and Fantasy 2017" (Edited with John Joseph Adams) (2017)
- "The Best Science Fiction and Fantasy of the Year: Eleventh Annual Collection" (Edited with Richard Chizmar) (2017)
- "The Best American Science Fiction and Fantasy 2016" (Edited with John Joseph Adams) (2016)
- "The Best Science Fiction and Fantasy of the Year: Tenth Annual Collection" (Edited with Richard Chizmar) (2016)
- "The Best American Science Fiction and Fantasy 2015" (Edited with John Joseph Adams) (2015)
- "The Best Science Fiction and Fantasy of the Year: Ninth Annual Collection" (Edited with Richard Chizmar) (2015)
- "The Best American Science Fiction and Fantasy 2014" (Edited with John Joseph Adams) (2014)
- "The Best Science Fiction and Fantasy of the Year: Eighth Annual Collection" (Edited with Richard Chizmar) (2014)
- "The Best American Science Fiction and Fantasy 2013" (Edited with John Joseph Adams) (2013)
- "The Best Science Fiction and Fantasy of the Year: Seventh Annual Collection" (Edited with Richard Chizmar) (2013)
- "The Best American Science Fiction and Fantasy 2012" (Edited with John Joseph Adams) (2012)
- "The Best Science Fiction and Fantasy of the Year: Sixth Annual Collection" (Edited with Richard Chizmar) (2012)
- "The Best American Science Fiction and Fantasy 2011" (Edited with John Joseph Adams) (2011)
- "The Best Science Fiction and Fantasy of the Year: Five Annual Collec