| 2018 | The Delirium Brief | Locus Awards source ↗ (opens in a new tab) | Finalist · Fantasy Novel | |
| 2018 | The Labyrinth Index | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Horror | |
| 2018 | Dark State | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2017 | The Nightmare Stacks | Locus Awards source ↗ (opens in a new tab) | Finalist · Fantasy Novel | |
| 2017 | The Delirium Brief | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Horror | |
| 2016 | The Nightmare Stacks | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Horror | |
| 2015 | The Annihilation Score | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Horror | |
| 2014 | Neptune's Brood | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2014 | Neptune's Brood | Hugo Award (book categories) source ↗ (opens in a new tab) | Finalist · Novel | |
| 2014 | Neptune's Brood | Locus Awards source ↗ (opens in a new tab) | Finalist · SF Novel | |
| 2014 | The Rhesus Chart | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Horror | |
| 2014 | The Rhesus Chart | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2013 | The Apocalypse Codex | Locus Awards source ↗ (opens in a new tab) | Winner · Fantasy Novel | |
| 2013 | The Rapture of the Nerds | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2013 | Neptune's Brood: A Space Opera | NPR Books We Love source ↗ (opens in a new tab) | Selection · Books We Love | |
| 2013 | Neptune's Brood | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2012 | Rule 34 | Locus Awards source ↗ (opens in a new tab) | Finalist · SF Novel | |
| 2012 | Rule 34 | Arthur C. Clarke Award source ↗ (opens in a new tab) | Shortlist · Novel | |
| 2012 | The Apocalypse Codex | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2011 | The Fuller Memorandum | Locus Awards source ↗ (opens in a new tab) | Finalist · Fantasy Novel | |
| 2011 | Rule 34 | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Science Fiction | |
| 2011 | Rule 34 | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2010 | Wireless | Locus Awards source ↗ (opens in a new tab) | Finalist · Collection | |
| 2009 | Saturn's Children | Hugo Award (book categories) source ↗ (opens in a new tab) | Finalist · Novel | |
| 2009 | Saturn's Children | Locus Awards source ↗ (opens in a new tab) | Finalist · SF Novel | |
| 2008 | Halting State | Hugo Award (book categories) source ↗ (opens in a new tab) | Finalist · Novel | |
| 2008 | Halting State | Locus Awards source ↗ (opens in a new tab) | Finalist · SF Novel | |
| 2007 | Glasshouse | Otherwise Award source ↗ (opens in a new tab) | Honor · Otherwise Award | |
| 2007 | Glasshouse | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2007 | The Jennifer Morgue | Locus Awards source ↗ (opens in a new tab) | Finalist · Fantasy Novel | |
| 2007 | Glasshouse | Hugo Award (book categories) source ↗ (opens in a new tab) | Finalist · Novel | |
| 2007 | Glasshouse | Locus Awards source ↗ (opens in a new tab) | Finalist · SF Novel | |
| 2006 | Accelerando | Locus Awards source ↗ (opens in a new tab) | Winner · SF Novel | |
| 2006 | Accelerando | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2006 | Accelerando | Hugo Award (book categories) source ↗ (opens in a new tab) | Finalist · Novel | |
| 2006 | Accelerando | Arthur C. Clarke Award source ↗ (opens in a new tab) | Shortlist · Novel | |