The massive project, which will link parts of Berkshire and Buckinghamshire to Essex via the centre of the capital, will be known as the Elizabeth line.
It is still under construction, and is set to open in December 2018.
London Mayor Boris Johnson made the announcement today as the Queen visited the under-construction Bond Street station.
She unveiled the purple Elizabeth line logo which will feature across the network, and wore an Angela Kelly lilac wool crepe dress with matching coat and hat for the occasion.
The Queen was taken in an industrial lift to the site 92ft below ground, where she viewed part of the railway tunnel and met construction apprentices dressed in bright orange jackets and trousers.
Mr Johnson said: “Crossrail is already proving a huge success for the UK economy and, as we move closer to bringing this transformative new railway into service, I think it”s truly wonderful that such a significant line for our capital will carry such a significant name from our country.
“As well as radically improving travel right across our city, the Elizabeth line will provide a lasting tribute to our longest-serving monarch.”
The Queen became the first reigning monarch to travel on the London Underground in 1969 when she opened the Victoria line.
In 1979 the Jubilee line was opened by the Prince of Wales, two years after celebrations to mark 25 years since the Queen”s accession to the throne.
Transport Secretary Patrick McLoughlin, who also attended the Crossrail event, described the naming of the Elizabeth line as “very fitting” given the Queen”s long association with UK transport.
The network will stretch from Reading and Heathrow in the west to Shenfield and Abbey Wood in the east.
A fleet of new 656ft (200m) long trains with nine walk-through air-conditioned carriages will run on the line.
The network will be opened in several phases, beginning with the Liverpool Street to Shenfield route in May next year.
Some 24 trains an hour will run in each direction in the central London tunnels when they open in December 2018. The full through service to Reading is due to begin in December 2019.