In a debate coinciding with one year until the referendum, Alex Salmond likened the policy to the poll tax and devolution in the 1990s.
He said independence would give Scots the power to decide for themselves on issues and create its own policies.
Mr Salmond said it was not disputed that Scotland could be a successful, economically independent country and with the opportunity of taking control of the powers needed to make decisions, he was confident that Scotland would vote yes next year.
Mr Salmond led the debate in the Scottish Parliament and said people will choose independence.
He said: "In the 1990s the poll tax became a totemic issue, a symbol of why devolution was necessary. The bedroom tax is becoming a symbol of why independence is needed.
"The UK government is implementing the bedroom tax at the same time that it is starting to replace Trident, at an estimated lifetime cost of £100bn.
"Instead of paying for and hosting Trident, while mitigating the effects of the bedroom tax, why don't we remove Trident, abolish the bedroom tax, and get on with building a better society for ourselves?"
The First Minister said independence would allow Scotland to create its own welfare policies and decide on taxation.
He said: "Independence is about the right to decide, the ability to make choices.
"And this government's argument is that the people who live and work in Scotland are the people who are most likely to make the right choices for Scotland."
Labour leader Johann Lamont rejected Mr Salmond's claim and said the UK had taken many progressive decisions of the last century.
Ms Lamont said: "That is an argument that points not only to Scotland leaving the United Kingdom, but to leaving Europe, the UN, and Nato too.
"If only Scotland can decide then no power to make decisions can rest anywhere else except Scotland, and that is a self-evident nonsense."
"The great changes in our history, the steps and progress in the lives of women, of people with disabilities, of people who suffer discrimination and disadvantage, in the huge issues of the environment and justice - these issues, these changes were won despite nationalism, not because of it.
"You win change, not by changing the constitutional arrangements of your country, but by winning the argument and proving you can create a better society."