There were no reports of injuries and the pilot ejected safely in the Wednesday incident, the authorities said.
The jet was coming in for a landing at Marine Corps Air Station-Yuma when it crashed in the backyard of a home less than 2km from the base, said Marine Corporal Michael Nease.
It was also carrying 300 rounds of 25-millimetre ammunition, he said.
There was no immediate word on the cause of the crash.
"I was just sitting here. It was a low soaring sound. It got real low, it was like a rumbling and I heard an explosion," said Marita Jane Wichman, who lives about four houses away from where the crash occurred.
Police said the house where the jet landed had been set on fire, but they did not have further details.
A 1.6-km radius around the crash site was evacuated while a military explosives disposal team was brought on the scene.
About 1300 people were evacuated, including a trailer park that is less than a block from the crash site, said Betty Conner, a training consultant for the Red Cross. A shelter was set up at a nearby school.
"I was just sitting here. It was a low soaring sound. It got real low, it was like a rumbling and I heard an explosion"
Marita Jane Wichman. resident
Nease said the pilot was the only person on board and was taken to hospital. His injuries appeared to be non-life threatening.
No one else was taken to the hospital as a result of the crash, a hospital spokeswoman said.
The AV-8B Harrier is a light attack aircraft that can take
off and land vertically like a helicopter.
Yuma is about 300km southwest of Phoenix and is near the Mexican border.