The accident happened in Shenley Fields Road, Selly Oak, at 13:40 BST, West Midlands Ambulance Service said.
The fire service used air bags to lift the tree and cutting equipment to free the man, who was taken to the Queen Elizabeth Hospital with head injuries.
Tree surgeons from Birmingham City Council also helped with the rescue, West Midlands Fire Service said.
The tree, thought to be more than 60ft (18m) high, collapsed during high winds.
A silvery blue Nissan car was directly underneath it when it came down and was "completely flattened", witnesses said.
Eye-witness Lucy Miller said: "There was a massive a gust of wind and a 60ft tree hit a smaller tree and both have landed on top of the car and crushed it outright".
Ms Miller said several people tried to help to lift the tree from the car but had to wait for the emergency services to arrive.
A West Midlands Ambulance Service spokesman said: "The driver, who had numerous injuries, including a head injury, was trapped in his car."
It was one of a number of trees that were brought down in the high winds.
In nearby Quarry Road, Weoley Castle, a tree fell on to two homes.
One of the owners Colin Smith said he was grateful that his family had not been inside at the time.
West Midlands Fire Service said crews had been called out to three incidents involving trees, including one that hit a car in Sutton Coldfield.
Some rail services were also affected across the West Midlands, with a fallen tree closing the line in Warwickshire.
A man has been seriously injured after his car was hit by a falling tree in Birmingham.