Saturday's launch was reportedly filmed as part of Homemade Astronauts, a new TV series about amateur rocket makers to be aired on the US Science Channel. The project had to be carried out on a tight budget.
With the help of his partner Waldo Stakes, Hughes was trying to reach an altitude of 5,000ft (1,525m) while riding his steam-powered rocket, according to Space.com.
In the video of the launch, a parachute can be seen trailing behind the rocket, apparently deployed too early, seconds after take-off.
In a tweet, the Science Channel said Hughes had died pursuing his dream.
San Bernardino County Sheriff's Department said its officers were called to a rocket launch event at around 14:00 local time (22:00 GMT) on Saturday.
The sheriff's office said "a man was pronounced deceased after the rocket crashed in the open desert". Hughes' publicist confirmed to US media outlets that it was the pilot who had been killed.
Darren Shuster, a former representative for Hughes, told TMZ the daredevil was "one-of-a-kind".
"When God made Mike he broke the mould. The man was the real deal and lived to push the edge. He wouldn't have gone out any other way! RIP" he said.
Mad Mike and his assistants built the homemade rocket in his backyard, spending around $18,000 (£14,000).
The rocket uses steam ejected through a nozzle for propulsion.
The daredevil, who lived in Apple Valley, made headlines internationally when he announced his intention to prove his theory that the Earth was flat.
In March last year, Hughes managed an altitude of 1,870ft (570m) before deploying his parachutes and landing with a bump.
Speaking afterwards, Hughes said: "Am I glad I did it? Yeah, I guess. I'll feel it in the morning. I won't be able to get out of bed. At least I can go home and have dinner and see my cats tonight."
He set a Guinness World Record in 2002 for the longest limousine jump - over 31 metres (103 ft) in a Lincoln Town Car stretched limo.
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