The 71-year-old musician - who was the frontman of the iconic group on-and-off from 1968 to 2004 - will be presented with the prestigious accolade at Shakespeare's Globe Theatre in London on September 1.
Anderson said he feels ''wonderful'' to be recognised for his impact on the alternative music genre both in Yes, his collaborations with Vangelis and his solo work.
And he feels ''blessed'' that he is still able to make music.
On receiving the title, he said: ''After all these years, it's just wonderful to be getting this very special award. Music has guided me along to this point in my life and I'm forever excited about the new and progressive musical adventures I am given by the 'Gods of Music'. Making music is like breathing to me, and I am blessed to be able to create music every day. A very grateful and humble thank you.''
Jerry Ewing, Editor of Prog Magazine, said: ''I suspect I speak for many Prog readers when I say that Jon Anderson has been at the very forefront of the progressive world that we've grown up with over the past 50 years. Either as a singer with the truly groundbreaking Yes, or as part of his series of albums with Vangelis, or as a solo artist in his own right. In today's musical world, his new album with Roine Stolt and his linking back up with Trevor Rabin and Rick Wakeman continue to thrust him to the forefront of the genre and send ripples of delight and intrigue amongst his millions of fans. He remains one of progressive music's key figures and a more than fitting recipient of the accolade Prog God.''
Meanwhile, Big Big Train, Dream Theater and King Crimson lead nominations all receiving three nominations each, and going head to head for Live Event and Band/Artist of the Year.
Anderson's honour comes not long after it was revealed himself and Yes' Trevor Rabin and Rick Wakeman are to reform under the new name ARW.
The 'Roundabout' hitmakers last performed together since 1990 when they did the Yes 'Union Tour'.
However, after a 25-year hiatus they will embark on a UK reunion tour kicking off on March 12 at Cardiff Arena and wrapping up at Manchester Apollo on March 25.
Progressive Music Awards in association with currencies.co.uk full list of nominations:
Limelight (New Band)
Tiger Moth Tales
The Aaron Clift Experiment
Rush - R40 Tour
Ramblin' Man Fair 2015
Big Big Train Live At King's Place
David Gilmour - Royal Albert Hall Shows
King Crimson - UK Tour
Opeth - Theatre Royal, Drury Lane
Steven Wilson - Royal Albert Hall Shows
Night Of The Prog 2015
Dream Theater - The Astonishing Live
The Fierce & The Dead
The Mute Gods
Hexvessel - 'Transparent Eyeball'
This Oceanic Feeling - 'Put Down The Gun'
Riverside - 'Towards The Blue Horizon'
Theo Travis' Double Talk - 'Smokin' At Klooks'
Bruce Soord - 'Field Day'
Headspace - 'Kill You With Kindness'
Andy Jackson - 'Drownings'
The Mute Gods - 'Praying To A Mute God'
Motorpsycho - 'Big Black Dog'
Knifeworld - 'I Must Set Fire To Your Portrait'
Album Of The Year
TesseracT - 'Polaris'
Hawkwind - 'The Machine Stops'
Dream Theater - 'The Astonishing'
Messenger - 'Threnodies'
iamthemorning - 'Lighthouse'
Big Big Train - 'Folklore'
Between The Buried & Me - 'Coma Ecliptic'
Purson - 'Desire's Magic Theatre'
Anderson/Stolt - 'Invention Of Knowledge'
Band / Artist Of The Year
Big Big Train
Between The Buried & Me
The Storm Thorgerson Grand Design Award
Peter Gabriel - 'Vinyl Reissues'
Anthony Phillips - 'Reissue Series'
Steve Hackett - Premonitions - 'The Charisma Years
Magma - Konzert Zund'
Opeth - 'Deliverance & Damnation'
King Crimson - 'Thrak Box'
Tony Banks - 'A Chord Too Far'
Irmin Schmidt - 'Electroviolet'
Porcupine Tree - 'The Delerium Years 1994-1997'
Rick Wakeman - 'Journey To The Centre Of The Earth Box Set'
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