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The 22-year-old arrives on what the Blue and Blacks call a "long-term deal" and will aim to make his debut after the November break for the Nations Championship.
Green, who played 30 times for Quins and signed a contract extension last December, joins after the announcement that George Nott will retire in December.
"He's a big, physical lock, standing over 6ft 7ins, and there's a nice weight to him, but the biggest thing is his rugby pedigree and his motivation," said Cardiff head coach Corniel van Zyl.
"As with any young second-row there is stuff to work on, but he has a huge appetite to improve."
Green was born in Sussex and qualifies for Wales through his mother's side of the family, with his parents now living in Gowerton.
He played for Wales in two World Rugby U20 Championships and was invited to train with the senior national squad during the 2024 Six Nations.
The lock is ready to battle with Teddy Williams, Josh McNally, Rory Thornton and Tom Manz for game time at Cardiff.
Green said: "The main things I bring are physicality and work rate, they are the two foundations I always review my performances against, so hopefully I can bring that to Cardiff.
"I am very grateful to Harlequins for the opportunities they have given me and I have loved my time there, but I'm now looking forward to the next chapter in my career and kicking on at Cardiff."
The Blue and Blacks are seventh in the United Rugby Championship (URC) and are next in action against Ulster at the Arms Park on Saturday, 5 December (15:00 GMT).