The explosion occurred at SpaceX's test site in Boca Chica, Texas, at approximately 4:30pm Eastern Time.
A company statement said there were no injuries, and said the mishap wasn't a serious setback.
"This had some value as a manufacturing pathfinder, but flight design is quite different", Musk wrote.
"The goal of today's test was to maximize the systems", said SpaceX spokesman.
SpaceX CEO Elon Musk indicated that the company will move on to more advanced Starship prototypes for future tests, as opposed to repairing the Mk 1 prototype. "The decision had already been made to not fly this test article". This was the vehicle that was revealed back in September.
The winged spacecraft stage, which was being tested without its conical nose section, remained upright on the test stand as vapor from a ruptured vessel towered out and down the vehicle's surfaces before it blew away.
Regarding the auto that exploded during the trial, company CEO Elon Musk told reporters in September that the vehicle could fly low in a few months and a version of the rocket could reach Earth's orbit in six months.
SpaceX's president and chief operating officer, Gwynne Shotwell, said Starship could take on such missions by 2022 - and take Japanese entrepreneur Yusaku Maezawa on a trip around the moon and back in 2023.
An inaugural test flight that involved the use of three Raptor engines should have taken place after the test, intending to reach an altitude of 20 kilometers (or approximately 12.5 miles). The system consists of two parts: The manned module, also known as Starship, and the rocket is known as Super Heavy.