The ad, created by , is part of an integrated campaign appealing for donations to the charity as the country faces a rise in repossessions at a time when there is already a massive waiting list for council accommodation.
The song 'Videotape' from the band's 2007 album plays while we pass through city landscape seen from a moving train.
Several of the buildings are made of playing cards and are blown away, while a voiceover by 'Minority Report' and 'Control' actress Samantha Morton says: "An estimated 75,000 homes will be repossessed this year, and nearly two million households await social housing.
"The housing crisis is real. Please help us to provide urgent advice and support. Text the word Shelter to 67777."
According to the charity this is the first time the band has allowed a song to be used in commercial advertising in the UK.
The band last year donated the music video for its song 'All I Need' to the MTV Exit campaign against human trafficking and exploitation.
Radiohead said: "We have always been big supporters of Shelter and believe that now more than ever urgently needs help and support to keep up its vital work."
The campaign also extends to posters on the London Underground and direct mail.