The crash on the Smiler ride injured 16 people and led to the closure of the park for five days last June.
Now the Health and Safety Executive has said that subsidiary Merlin Attractions Operations Ltd will face legal action.
Neil Craig, head of operations for HSE in the Midlands said:
“We have today informed Merlin Attractions Operations Ltd that it will be prosecuted for breaching health and safety law.
“This was a serious incident with life-changing consequences for five people.
“We have conducted a very thorough investigation and consider that there is sufficient evidence and that it is in the public interest to bring a prosecution.”
Merlin has yet to comment.
The news came on the same day that parent company Merlin Entertainments announced its full-year results.
Operating profit fall by 6% after experiencing what it called the “most difficult year” in its history.
Visitor numbers across the whole company were up fractionally to 62.9 million while revenue across the group rose 2.3% to £1.3 billion for the year to December 26, 2015.
Despite the increase, operating profit declined from £311 million to £291 million.
Resort Theme Parks Operating Group revenue fell by 12.4% on a like-for-like basis due to the Alton Towers incident.
Chief executive Nick Varney said: "Despite a challenging year, the business delivered a robust performance in 2015.”
Meanwhile, Merlin has announced the acquisition of a 15% stake in sightseeing company Big Bus Tours.
