Thames Valley Police said it happened at about 12:00 BST on Saturday. The pilot has been taken to John Radcliffe Hospital, but the extent of his injuries is unknown.
The new-build block of flats off Camp Road, Upper Heyford, were unoccupied and officers said nobody else was hurt.
An eye witness described seeing the pilot parachuting down on to the old RAF base.
Tisa Kilby, 55, said she was out walking her dogs when she saw the light aircraft hit the building.
“I looked up and literally saw this guy leap out of this plane and thought, that’s an odd place to be parachuting,” she said.
“Within four or five seconds the plane nose-dived and crashed into the block of flats.”
Ms Kilby said she had been told by police at the scene that the pilot had suffered life-changing injuries
South Central Ambulance Service said the victim, an “older gentleman” was treated at the scene before being taken to hospital.
The Air Accidents Investigation Branch (AAIB) has launched an investigation and inspectors have begun searches.