Ferguson became host of the series in 2005. Previous hosts of the show were Tom Snyder and Craig Kilborn.
Ferguson's milestone episode as the show's star is to air Tuesday.
"Those incorrigible bags o' fun, 'The Late Late Show' puppets, will take over the show for the 1,000th episode," the network said in a news release. "Wavy, the crocodile puppet, will serve as the host of the show as he welcomes guests Kristen Bell, Maria Bello and Jason Schwartzman. The musical guest is a performance of 'Dracula's Lament' by Jason Segel with his puppet, Dracula, from the film 'Forgetting Sarah Marshal' and the band The Broken West."