McAvoy, 39, will play Lord Asriel – the uncle of the story’s young protagonist Lyra, who will be portrayed by one of the stars of X-Men spin-off film Logan, Dafne Keen, 13.
Luther star Ruth Wilson will appear as Mrs Coulter – the former lover of McAvoy’s character who enters Lyra’s life as she embarks on an intrepid journey of discovery form her home in Jordan College, Oxford, to London.
Duff will play the role of Ma Costa, who is one of the boat-dwelling characters known as Gyptians who transport Lyra to the Arctic during her epic quest.
The Wire’s Clarke Peters and Game of Thrones’ Ian Gelder are also set to appear.
New Line Cinema is producing the series with production company Bad Wolf for BBC One.
It marks the Hollywood studio’s first venture in British television.
The series will be filmed in Cardiff at Wolf Studios Wales and principal photography has already begun.
Carnegie Medal-winning novelist Pullman said: “I’m delighted that the production is underway and I’m looking forward immensely to seeing how it looks.
“Bad Wolf has assembled a wonderful cast and I’m sure every His Dark Materials reader is as keen as I am to see it all coming together.”
The first series of the TV adaptation will tell the story of the trilogy’s first instalment Northern Lights before the plot moves on to dramatise its follow-ups The Subtle Knife and The Amber Spyglass.
It will be directed by Academy Award winner Tom Hooper, who helmed The King’s Speech.
Pullman’s books have been adapted for the small screen by Bafta-winning screenwriter Jack Thorne.
Controller of BBC Drama Piers Wenger said: “The vast, complex and deeply imaginative landscape of Philip’s novels requires a world class, but quintessentially British band of creatives to bring them to life.
“The BBC is proud and privileged to be the host to such visionaries.”
His Dark Materials has been published in more than 40 languages and has sold worldwide close to 18 million copies.
The characters from Pullman’s books previously appeared in the 2007 film adaption of Northern Lights called The Golden Compass, which starred Nicole Kidman, Daniel Craig and Sir Ian McKellen.
In 2016 McAvoy and Duff announced their split after ten years of marriage.
The couple have a son, Brendan, who was born in 2010. The pair met while starring in Channel 4 series Shameless together.
Duff told the Sunday Telegraph’s Stella Magazine in May 2017 that during their divorce there was still “a lot of good will” between the pair and that they “laugh all the time”.