Cox was attacked with a knife and a firearm outside her constituency surgery in the village of Birstall, northern England, on Thursday.
Her murder has sent shockwaves through British politics and drawn messages of condolence from around the world, with US President Barack Obama condemning the "heinous" attack.
Campaigning ahead of Thursday's closely-contested referendum on Britain's membership of the European Union remains suspended Saturday as a mark of respect.
Mair, 52, who is from Birstall, a quiet village in the Yorkshire hills, was arrested Thursday close to the scene of the attack.
West Yorkshire Police's Detective Superintendent Nick Wallen, who is leading the investigation, said in a brief statement that Mair had been charged with a string of crimes related to the Labour MP's death.
Mair is due to appear in a central London court later Saturday.
"We have now charged a man with murder, grievous bodily harm, possession of a firearm with intent to commit an indictable offence and possession of an offensive weapon," he said.
"Thomas Mair, 52, of Birstall, will appear at Westminster Magistrates Court today."
Prime Minister David Cameron and opposition Labour leader Jeremy Corbyn laid bouquets at a massive floral tribute to Cox in Birstall on Friday.
"Where we see hatred, where we find division, where we see intolerance, we must drive it out of our politics and out of our public life and out of our communities," Cameron said.
"Today our nation is rightly shocked," he said.
Tribute from Obama
The White House said Obama offered condolences to Cox's widower and praised her "selfless service".
Obama called Brendan Cox while travelling on the Air Force One presidential plane.
"President Obama offered his sincere condolences on behalf of the American people to Mr Cox and his two young children, as well as to her friends, colleagues and constituents," the White House statement said.
"The president noted that the world is a better place because of her selfless service to others, and that there can be no justification for this heinous crime, which robbed a family, a community and a nation of a dedicated wife, mother and public servant."
Cox, a former aid worker who was campaigning for Britain to stay in the EU and also spoke out for Syrian refugees, was killed just a few miles (kilometres) from where she was born.
Eyewitness Hichem Ben Abdallah, 56, told AFP he heard two shots and saw her on the ground.
"Her face was full of blood," said Ben Abdallah, who campaigned alongside the Labour politician before she was elected to parliament for the first time last year.
A fund created in Cox's memory by her friends and family has raised more than £200,000 ($290,000, 250,000 euros) so far for charities close to her heart.
The money will support the Royal Voluntary Service which helps combat loneliness in her constituency; the Hope Not Hate anti-extremism group and the White Helmets volunteer search and rescue workers in Syria.
Vigil outside parliament
At a vigil in London's Parliament Square on Friday evening, hundreds of people gathered to lay flowers and pay their respects, holding a minute's silence.
Former Labour leader Ed Miliband joined former deputy leader Harriet Harman and Labour MP Wes Streeting in paying tribute to Cox.
"Her legacy of giving a voice to the voiceless, particularly those caught up in war and in conflict, her legacy of standing up against oppression wherever she found it, and her legacy of preaching the values of unity and not division," said Miliband.
"Jo Cox only loved, she never hated."
Streeting added: "What we can all do here today is pledge ourselves in any way that we can to make the world that Jo was fighting for.
"A world of humanity, of decency, of compassion, of solidarity, of human rights, and social justice, simple kindness."
Cox is the first female British MP to be murdered.
The last British lawmaker killed in office was Ian Gow, who was assassinated by Irish Republican Army paramilitaries in a car bomb attack in 1990.
Cox lived with her husband Brendan and their two children, aged three and five, on a houseboat moored on the River Thames in London, close to the city's iconic Tower Bridge.
Mourners laid flowers on the roof of the converted barge along with pictures of the slain MP.
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