The charity says its research suggests 150,000 women will be around £3,500 a year worse off when the new universal credit takes effect next year.
Single mums on low incomes would be forced to make ends meet by either working longer hours or by getting into debt, the charity claims.
Chief executive of Save the Children Justin Forsyth said: "Universal credit will help some families, but mums working hard to stay above the breadline are its big blind spot.
It's incredibly hard bringing up three kids on £370 a week - losing almost a fifth of that will push many families over the edge.
"The Government must make sure mums who want to work keep more of their incomes and get more support with childcare.
"Otherwise we'll see fewer women in the workplace and more children growing up in poverty."
The charity's report - Ending Child Poverty - claims the changes would make it less attractive for parents to come off benefits and into work because of poor childcare support.
The charity is organising a Mums United campaign on Mother's Day to try to persuade Chancellor George Osborne to stop the changes ahead of next week's budget.
Kym Marsh said: "Having been a single mum on benefits I completely understand when they say that the best chance kids have of not growing up in poverty is if their mums can work.
"The problem, though, is not just the cost of childcare – every mums nightmare!– but also that the Government's new welfare reforms coming in are going to mean work won't pay for some of the poorest mums out there. So what happens to them and their kids?"
But the Department for Work and Pensions said 600,000 lone parents would be better off under a system that "incentivised work and made work pay".
By the time universal credit is fully implemented, the Government expects 900,000 people to be lifted out of poverty.
A spokeswoman for the DWP said the Save the Children's claims were based on hypothetical examples and it was wrong to assert that lone parents would lose out under universal credit.
"The truth is 600,000 lone parents will be better off under a system which will incentivise work and make work pay", a spokeswoman told the BBC.
"This is in stark contrast to the broken system this government inherited which only rewards lone parents who work 16 hours or more.
"Under universal credit 80,000 more families, including lone parents, will be able to claim childcare support - no matter how few hours they work," she added.
Shadow employment minister Stephen Timms said the government must work harder to get universal credit right.
"The best way to get children out of poverty is to get more parents in work," he said.
"But as this report shows, their current plans will lock in a parents' penalty, chip away at the incentives for thousands to work and push 150,000 working parents deeper into poverty."
What do you think? Will you be affected by the changes?
More on Parentdish: Universal credit: Why 150,000 working mums will be worse off