The automobile, worth an estimated $400,000 to $600,000, is being sold under Christie's The Exceptional Sale, described by the auction house as "a highly selective, tightly curated auction of decorative arts masterpieces and significant cultural icons".
"This Aston Martin Vanquish is a tour de force of automobile engineering and a distinct pleasure to drive," Craig said.
"While I will miss it, I am keen to further the very important work of The Opportunity Network with its sale," he added.
Craig, 49, worked with Aston Martin's design chief to customize his personal vehicle.
The actor had made his debut as Agent 007 in "Casino Royale" (2006) and also played the character created by Ian Fleming in "Quantum of Solace" (2008), "Skyfall" (2012) and "Spectre" (2015).
Last August, Craig ended months of speculation over who would star in the next film in the James Bond series, confirming he would return as Agent 007 in the next, yet-untitled installment.