Bolton, who has long advocated a tougher line on dealing with Tehran, told a fringe meeting at Britain's main opposition Conservative Party's annual conference that time was running out to halt Iran's alleged weapons ambitions.
"Life is about choices, and we are very close to the point where we have to make that choice on military force," Bolton told delegates in the northern coastal holiday town of Blackpool.
"This is not an attractive option, but after four-plus frustrating years watching European diplomacy fail time and time again and watching our options more and more constrained, I do not know what the alternative is."
The often outspoken ex-ambassador has criticized Britain and European allies over their approach to dealing with Tehran. Iran has refused to halt a uranium enrichment program and denied claims by the US and others that it is seeking to develop nuclear weapons.
"If the choice is between an Iran with nuclear weapons and the use of military force to prevent that... then I think we have to look at a limited strike against their nuclear facilities," Bolton told the meeting.
Bolton told delegates, "The US once had the capability to engage in the clandestine overthrow of governments, I wish we could get it back," winning applause and cheers.
"If we were to strike Iran it should be accompanied by an effort at regime change as well, because I think that really sends the signal that we are not attacking the people, we are attacking the nuclear weapons program," he said.
According to The Guardian, Bolton also praised the French president Nicolas Sarkozy and his forthright criticism of Iran in recent weeks.
Sarkozy recently called for tougher international sanctions against Iran's nuclear program and warned French oil giant Total and gas firm Gaz de France to refrain from investing in Iran.
Ynet contributed to this report