Carrie and Tim Morris from Booka picked up the prestigious national prize at a glamorous awards ceremony at The Hilton in London.
Mr Morris said: "It was fantastic. It really was a night to remember. You enter these award competitions and you hope beyond hope that it might be you that wins. When it is, it's very unexpected. I don't think it's fully sunk in yet.
"We were absolutely thrilled and delighted and very proud."
The Church Street shop had already been named this year's best independent bookshop in the Midland and Wales for the second year running.
That award meant the business was shortlisted for the national award.
Judges in the competition said they were looking for "simply the best all-round independent bookshop in Britain".