Scruton was sacked from the role of chair over "unacceptable" comments made in an interview about Hungarian jews, Muslims, and Chinese people. The ministry of housing said that a permanent chair would be announced in due course.
"I look forward to leading the commission in the interim, using my and fellow commissioners' experience and expertise to champion beauty in the built environment, said Boys Smith.
Boys Smith's institute promotes low rise development
Boys Smith is already a commissioner for the Building Better, Building Beautiful Commission, an independent body set up to advise the government on the design of new build homes in the UK.
He is best known for setting up Create Streets, a research institute that supports "community-led regeneration" and prioritises high-density, low-rise buildings over tower blocks.
"The commission has an integral role in ensuring the homes communities need are built, accepted and loved by those who live in and near them," said UK housing secretary James Brokenshire.
"I am delighted that Mr Boys Smith has agreed to step into the role as interim chair and continue to advance this important work."
Responding to the announcement Ben Derbyshire, president of the Royal Institute of British Architects (RIBA) tweeted to urge Boys Smith to be impartial in his new role.
"I have warned Nicholas Boys Smith against casting our profession as an obstacle to progress," he said.
"Now I shall write to him urging impartiality as acting chair of [the] Commission. He must listen to the wise counsel of Paul Monaghan and Sunand Prasad on his panel."
Housing secretary "saddened" by Scruton sacking
Brokenshire announced Boys Smith's appointment as acting chair in an LBC radio interview, where he said he was "saddened by the whole situation" that led to the removal of the original chair.
Scruton was appointed chair of the Building Better, Building Beautiful Commission in November 2018. He was removed from the role last month after an interview in New Statesman where he made comments about a "Soros empire" and said the Chinese government was turning its citizens in to replicants.
Brokenshire said the New Stateman's story, as well as the criticism surrounding Scruton's appointment last year, had been a "complete distraction" from the work of the commission.
The minister had previously defended Scuton's appointment when Labour MPs called for his sacking over comments about homosexuality being abnormal and calling date rape a myth.
"It is just that regret that I have, and I have a huge amount of respect for Sir Roger's focus on aesthetics, how he is a leader in his field, all those things that I wanted him to do for the project," said Brokenshire.
The Building Better, Building Beautiful Commission has been divisive from the outset. When appointed, Scruton told Dezeen that he viewed his role as chair was to protect the British public from architects imposing their values over popular taste.
Housing minister Kit Malthouse has since tried to make amends, calling on architects to join him and the Commission to push back against bland developer-led projects.
Main image courtesy of Create Streets.