The Late Late Show host started to use puppets in the opening of his CBS programme in 2008.
Ferguson, who welcomed a baby boy earlier this year, told Playboy: "That has a complicated backstory. It started with a buddy of mine named Steve Jones, the guitarist with the Sex Pistols. He had a radio show in Los Angeles called Jonesy's Jukebox, and he'd play all these records from his collection.
"I was driving to work one day, listening to his show, and he was playing 'The Lonely Goatherd' from The Sound of Music. [sings] 'High on a hill was a lonely goatherd / Lay ee odl lay ee odl lay hee hoo.' It just made me laugh.
"So I came to work and said, 'You know what? I'm going to lip-synch that 'Lonely Goatherd' song on tonight's show.' There were these hand puppets lying around the office, and we used them for the bit. That was kind of the beginning of it."
When asked what it is about the puppets that he liked, Ferguson said: "I like things that are different and weird. When I was first trying out for the show, I remember thinking, 'If I ever do this, I want it to be something f**king different'.
"There are too many of these shows already. I don't want to be like everybody else. Let's f**k with people's expectations. If there has to be a sidekick, then let's make it a robot skeleton."
Back in August, Ferguson and his staff had an anthrax scare when two employees opened a letter containing white powder and threatening messages.
After an investigation, the police determined the powder as cornmeal and not anthrax.
Watch a video of Craig Ferguson's puppets below: