| Year | Association | Category | Nominated work | Result |
| 1985 | Academy of Country Music | Top New Male Vocalist | Marty Stuart | Nominated |
| 1990 | Country Music Association | Video of the Year | "Hillbilly Rock" | Nominated |
| 1991 | Academy of Country Music | Top Vocal Duet | Marty Stuart and Travis Tritt | Nominated |
| 1992 | Nominated |
| Grammy Awards | Best Country Collaboration with Vocals | "The Whiskey Ain't Workin (with Travis Tritt) | Won |
| Country Music Association Awards | Vocal Event of the Year | "The One's Gonna Hurt You" (with Travis Tritt) | Won |
| 1994 | Album of the Year | Asleep at the Wheel: Tribute to the Music of Bob Wills & the Texas Playboys | Nominated |
| Rhythm, Country and Blues | Nominated |
| Vocal Event of the Year | "The Devil Comes Back to Georgia" (with Charlie Daniels Band, Travis Tritt, Mark O'Connor and Johnny Cash) | Nominated |
| 1996 | Vocal Event of the Year | "Honky Tonkin's What I Do Best" (with Travis Tritt) | Nominated |
| Academy of Country Music | Top Vocal Duet | Marty Stuart and Travis Tritt | Nominated |
| 1998 | Vocal Event of the Year | Same Old Train (with various artists) | Won |
| 1999 | Grammy Awards | Best Country Collaboration with Vocals | Won |
| Country Music Association | Vocal Event of the Year | Nominated |
| 2000 | Golden Globe Awards | Best Original Score | All the Pretty Horses | Nominated |
| 2002 | Grammy Awards | Best Country Instrumental Performance | "Foggy Mountain Breakdown" | Won |
| 2004 | International Bluegrass Music Awards | Recorded Event of the Year[A] | Livin', Lovin', Losin': Songs of the Louvin Brothers | Won |
| 2005 | Americana Music Honors & Awards | Lifetime Achievement Award for Performance | Marty Stuart | Won |
| 2008 | International Bluegrass Music Awards | Recorded Event of the Year[B] | Everett Lilly & Everybody and Their Brother | Won |
| 2011 | Grammy Awards | Best Country Instrumental Performance | "Hummingbyrd" | Won |
| Best Country Collaboration with Vocals | "I Run To You" (with Connie Smith) | Nominated |
| 2017 | Americana Music Honors & Awards | Duo/Group of the Year | Marty Stuart and his Fabulous Superlatives | Won |
