The former Conservative prime minister died of a stroke last Monday aged 87. She will be given a ceremonial funeral with military honours, one step down from a state funeral.
It is the first time that the bells of Big Ben and the Great Clock at the Palace of Westminster will have been halted in this way since the funeral of Winston Churchill in 1965.
The announcement came from John Bercow, the speaker of the House of Commons, in a statement to MPs, many of whom had asked the parliamentary authorities to make a special tribute to the former prime minister, the Telegraph reported.
"The most appropriate means of indicating our sentiments would be for the chimes of Big Ben and the chimes of the Great Clock to be silent for the duration of the funeral proceedings," he said.
"I have therefore made the necessary arrangements to achieve this. I believe there can be a profound dignity and deep respect both expressed in and through silence and I am sure that the House will agree," Bercow said.
Francis Maude, the cabinet office minister coordinating arrangements for the funeral, welcomed the decision.
"As you know, Lady Thatcher held Parliament in very great reverence in her time both in this House and in the Lords and I am confident that this will be seen as a very dignified and respectful gesture on behalf of parliament and I am very grateful to you," Maude told the Commons.
David Cameron's official spokesman said, "It is not surprising that a good number of people wish to commemorate Lady Thatcher's passing."
The name 'Big Ben' is often used to describe parliament's famous clock tower, which was recently re-named ElizabethTower in honour of the Queen.
Gandhi and Thatcher: Were two 'Iron Ladies' too many?
The notorious link that Modi and Thatcher share
When Thatcher praised Rajiv, Manmohan for liberalisation
Thatcher, a British leader who was both loved and hated
British Iron Lady Margaret Thatcher dies after stroke