YMCA's Uncertain Futures report said the changes planned include removing the automatic entitlement to Housing Benefit for young people who find themselves out of work and claiming Universal Credit.
The charity has warned this could force thousands of vulnerable young people onto the streets.
YMCA researchers said that contrary to the perceptions of many, increasing numbers of young people are now staying at home for longer and opting not to claim benefits, while the small numbers who do move out and claim are increasingly doing so for shorter periods of time.
The research said without the right protections the Government "is in danger of exposing many of the most vulnerable young people to the risk of becoming homeless".
It added the majority of 18 to 21-year-olds currently claiming unemployment and housing benefits either had dependent children, have recently left care or had been thrown out by their parents.
Denise Hatton, Chief Executive of YMCA England, said: "As the report we launched today shows, in seeking to tackle those small numbers taking advantage of the system, the Government is in real danger of inadvertently taking away support from some of the country's most vulnerable young people.
"In removing automatic entitlement to Housing Benefit, young people could face the prospect of losing not only a safety net but also a springboard that helps get them up and get their lives back on track.
"Unless firm and clear exemptions are put in place, thousands of young people who don't have the option to go home will be left to face uncertain futures."
The charity said one of the people it helped, Sam, would be left homeless by the new rules, due to be introduced in 2017.
He was privately educated and went to YMCA after suffering from mental health issues following the breakup of his parents' marriage.
He said: "What about the people who have no choice, what about the people who have got nowhere to go but places like YMCA?
"It's a roof over your head, which for most people, is only payable with the help of Housing Benefit. Without Housing Benefit there would be a lot more people on the streets"
Listen to Premier's Antony Bushfield speaking to YMCA Director of Policy Jason Stacey:
The government's reforms to Housing Benefit will not remove affect existing claimants, and will only apply to unemployed claimants from April 2017.
Care-leavers, those unable to work because of disability, and those with children are also exempt. Young people who have been working for six months previously will also still be able to claim Housing Benefit.
A DWP Spokesman said: "This report is deliberately misleading since we have been very clear that vulnerable young people including care leavers and people with children will be exempt from this policy.
"We want to make sure young people get the support they need to move into work and do not slip straight into a life on benefits."