Mrs Cox, 41, died after being shot and stabbed in the street outside her constituency surgery in Birstall, near Leeds, last Thursday.
Thomas Mair, 52, from Birstall, is charged with murder, grievous bodily harm, possession of a firearm with intent to commit an indictable offence and possession of an offensive weapon.
At an initial hearing at Westminster Magistrates’ Court on Saturday, Mair refused to give his name, instead saying he was called “Death to traitors, freedom for Britain”.
When asked to confirm he was Thomas Mair at the Old Bailey on Monday, he replied: “Yes, I am.”
He made his first crown court appearance before Mr Justice Sweeney via video link from top security Belmarsh prison.
Grey-bearded Mair sat with his arms folded beside a prison officer. He wore beige trousers and a white long-sleeved t-shirt.
There was no application for bail and he was remanded in custody.
He will appear at the same court for a preliminary hearing before Mr Justice Saunders at 10am on Thursday.
The case is being heard under the terrorism protocol.