The North Charleston Fire Department said that the collision was first reported to emergency dispatchers shortly before 2:30 a.m.
The three people who were killed were pronounced dead at the scene and were among the four occupants of the SUV that was struck by the train. The fourth person was taken to a hospital.
An Amtrak spokesperson said in an emailed statement that Auto Train 53 was traveling from Lorton, Virginia to Sanford, Florida.
The train, which had 474 passengers in 12 of its cars, made a controlled emergency stop after colliding with the SUV, the spokesperson said, adding that none of the passengers or crew were injured.
Amtrak representatives are assessing damage to the train.
The North Charleston Police Department and CSX Transportation are investigating the cause of the crash.
The Associated Press contributed to this report.
From The Epoch Times