Filmography
| Year | Title | Role |
| 2026 | The Odyssey (2026) | Odysseus |
| 2026 | The Rip | Lieutenant Dane Dumars |
| 2025 | The Accountant 2 (2025) | Executive Producer |
| 2025 | Kiss of the Spider Woman (2025) | Executive Producer |
| 2024 | Drive-Away Dolls (2024) | Senator Gary Channel |
| 2024 | IF (2024) | Flower |
| 2024 | The Instigators (2024) | Rory |
| 2024 | Small Things Like These (2024) | Producer |
| 2023 | Oppenheimer (2023) | Leslie Groves Jr. |
| 2023 | Air (2023) | Sonny Vaccaro |
| 2023 | Kiss the Future (2024) | Producer |
| 2021 | Stillwater (2021) | Bill Baker |
| 2021 | The Last Duel (2021) | Jean de Carrouges |
| 2019 | Ford v Ferrari | Carroll Shelby |
| 2019 | Jay & Silent Bob Reboot | Loki |
| 2018 | Deadpool 2 | Redneck No. 1 |
| 2017 | Downsizing | Paul |
| 2017 | Bending the Arc | Executive Producer |
| 2017 | Suburbicon | Gardner |
| 2017 | Boston (2017) | Narrator |
| 2016 | The Great Wall (2017) | William Garin |
| 2016 | Manchester By the Sea | Producer |
| 2016 | Jason Bourne | Jason Bourne |
| 2016 | Backpack Full of Cash | Narrator |
| 2015 | The Martian | Mark Watney |
| 2014 | The Monuments Men | James Granger |
| 2014 | Interstellar (2014) | Dr. Mann |
| 2013 | Elysium | Max |
| 2013 | Behind the Candelabra | Scott Thorson |
| 2013 | The Zero Theorem | Management |
| 2012 | Promised Land | Steve Butler |
| 2012 | Radioman | Actor |
| 2011 | Margaret (2011) | Mr. Aaron |
| 2011 | The Adjustment Bureau | David Norris |
| 2011 | Contagion | Mitch Emhoff |
| 2011 | We Bought a Zoo | Benjamin Mee |
| 2011 | His Way | Self |
| 2011 | American Teacher | Narrator |
| 2011 | Happy Feet Two in 3D | Bill the Krill |
| 2010 | Green Zone | Roy Miller |
| 2010 | True Grit (2010) | LaBoeuf |
| 2010 | Inside Job | Narrator |
| 2010 | Hereafter (2010) | George Lonegan |
| 2009 | The Informant! | Mark Whitacre |
| 2009 | Invictus | Francois Pienaar |
| 2008 | Running the Sahara | Executive Producer, Narrator |
| 2008 | Ponyo (2009) | Koichi |
| 2007 | Ocean's Thirteen | Linus Caldwell |
| 2007 | The Bourne Ultimatum | Jason Bourne |
| 2006 | The Good Shepherd | Edward Wilson |
| 2006 | Feast | Executive Producer |
| 2006 | The Departed | Colin Sullivan |
| 2005 | Syriana | Bryan Woodman |
| 2005 | The Brothers Grimm | Wilhelm Grimm |
| 2004 | Jersey Girl | PR Exec #2 |
| 2004 | Eurotrip | Donny |
| 2004 | The Bourne Supremacy | Jason Bourne |
| 2004 | Ocean's Twelve | Linus Caldwell |
| 2004 | Howard Zinn: You Can't Be Neutral on a Moving Train | Narrator |
| 2003 | The Battle of Shaker Heights | Executive Producer |
| 2003 | Stuck on You | Bob Tenor |
| 2002 | The Bourne Identity | Jason Bourne |
| 2002 | Stolen Summer | Producer |
| 2002 | The Third Wheel | Kevin |
| 2002 | Spirit: Stallion of the Cimarron | Spirit |
| 2002 | Confessions of a Dangerous Mind | Bachelor n. 2 |
| 2001 | Jay and Silent Bob Strike Back | Himself / Will Hunting |
| 2001 | Ocean's Eleven (1960) | Linus Caldwell |
| 2000 | Titan A.E. | Cale |
| 2000 | The Legend of Bagger Vance | Rannulph Junuh |
| 2000 | All the Pretty Horses | John Grady Cole |
| 1999 | The Talented Mr. Ripley | Tom Ripley |
| 1999 | Dogma: Resurrected! A 25th Anniversary Celebration (2025) | Loki/Larry |
| 1998 | Saving Private Ryan | Private James Francis Ryan |
| 1998 | Rounders | Mike McDermott |
| 1997 | Good Will Hunting | Will Hunting |
| 1997 | The Rainmaker | Rudy Baylor |
| 1993 | Geronimo: An American Legend | Lt. Britton Davis |
| 1992 | School Ties | Charlie Dillon |
