The Virgin Group boss said about 20 people, including Winslet and her children, were staying in the eight-bedroom Great House on Necker, his private isle in the British Virgin Islands.
Branson said he was staying in another property around 100 yards (meters) away with his wife, Joan and son Sam, 25.
He said the fire broke out around 4 a.m. during a tropical storm with lightning and high winds, and Sam managed to help evacuate Winslet and other guests from the house.
Tropical Storm Irene walloped the Virgin islands and headed towards Puerto Rico late Sunday and early Monday, strengthening into a hurricane Monday with winds of about 80mph (130 kph), according to the U.S. National Hurricane Center.
Branson said the guests, including his 90-year-old mother and his daughter Holly, 29, all managed to get out safely.
"Kate Winslet, her boyfriend and her family were there and Holly and some of her friends were also staying," Branson said.
"My mother was there and they managed to get her out and she is fine."
Winslet's spokeswoman, Sara Keene, confirmed the actress was unharmed.
Branson said the house was "completely destroyed" and the fire was not entirely out Monday.
"My office was based in the house and I have lost thousands of photographs which is very sad," Branson said.
He said he planned to rebuild the house "as soon as we can."
"We'll all stay here for the time being," he said. "There's a lot of damage and we won't be able to stick it back together again right away."
Virgin said the cause of the fire was still being investigated but lightning was the likely culprit.
Branson, 60, bought the island in the early 1980s and began building the Great House in 1982. He also has developed an exclusive eco-resort on the island showcasing renewable energy technology.
Winslet, 35, shot to international stardom with her appearance opposite Leonardo DiCaprio in James Cameron's "Titanic," and sealed her reputation with a best actress Academy Award in 2009 for "The Reader."
She has two children, 10-year-old Mia and Joe, 7, from marriages to directors Jim Threapleton and Sam Mendes.