Firefighters were alerted to the blaze when a woman was woken by burning embers falling from her bedroom ceiling.
The 61-year-old man was found in the first floor of a mid-terrace property in Winchester Road at about 03:45 BST.
He later died in hospital and an investigation is under way to determine the cause of the fire. The man's family have been informed.
The woman who called 999 was also taken to hospital by South Central Ambulance for smoke inhalation.
A spokesperson for Hampshire Fire and Rescue said all other residents of the property were accounted for.
They added: "Every fire is a reminder of the importance of home fire safety and the importance of fitting and maintaining smoke alarms and ensuring your escape routes are clear."
A man has died in a "severe" flat fire in Southampton.