The singer-songwriter, 41, is the first person to twice receive the UK's top musical award, which started in 1992. Her CD Let England Shake, inspired by war and boosted by good reviews, was the favourite in betting.
A decade ago, she was the first female Mercury winner, with Stories From the City, Stories From the Sea, a record based on her affection for New York.
"It's really good to be here this evening," she told the audience in London's Grosvenor House hotel. Harvey was on tour and unable to attend when she last won on September 11, 2001, "in Washington D.C., watching the Pentagon burning from my hotel window. So much has happened since then," she said.
The winning album, on Island Records, is experimental rock with greatest resonance in the UK, featuring state-of-the-nation titles such as The Glorious Land, England and The Last Living Rose. Harvey sings: "Take me back to beautiful England/and the grey, damp filthiness of ages." The judges said the CD is "gripping and profound."
Let England Shake was recorded in a Dorset church and features three of Harvey's long time collaborators: Mick Harvey, John Parish and Flood, all of whom contribute to a collection of songs that touch upon the futility of war, what it means to be English and British history.
It was released in the UK in February 2011 and includes the single The Words that Maketh Murder — the second of which Harvey performed during the ceremony.
"This album took me a long time to write and it was very important to me," said Harvey onstage. "I wanted to make something that was meaningful not just for myself, but for other people and hopefully to make something that will last."
The Mercury has often been given to new or non-commercial acts and pits different genres against one another, ranging from folk and jazz to hard rock and classical. The winner receives £20,000 (Dh117,428), although the boost from album sales can be worth much more.
The 12 shortlisted albums racked up an additional 400,000 sales between the list being announced in July and the ceremony, the UK Official Charts Co. said in an e-mail on Tuesday.
Musical Quality
The award focuses on musical quality and doesn't take into account sales, media profile or live performances, according to a statement by the judges, a mixture of critics and music industry figures. Commercial acts such as Adele, Amy Winehouse and Robbie Williams have often lost out to cutting edge performers such as Harvey.
All of the nominated acts performed at the ceremony apart from Adele, who apologised and said she was temporarily unable to sing because of a bad throat infection.
The singer said she was "gutted" not to be able perform, reported the Guardian, adding she also used one of her "signature expletives". "It makes me breathless," she said of not performing.
While the Mercury judges are known for their surprise choices, this is the second straight year that the favourite has won. Last year, London band the xx triumphed with its debut CD of understated indie rock. There were surprise winners in 2009 (Speech Debelle), 2008 (Elbow) and 2007 (Klaxons).
The event has been held annually since 1992, when Scottish rockers Primal Scream took home the inaugural award for Screamadelica. Previous winners also include Pulp (Different Class) in 1996, Dizzee Rascal (Boy in da Corner) in 2003 and Arctic Monkeys (Whatever People Say I Am, That's What I'm Not) in 2006.
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