The Health & Safety Executive (HSE) said the Merlin company responsible for the Staffordshire attraction, Merlin Attractions Operations, would appear in court in Newcastle-under-Lyme on April 22.
Two female passengers on the ‘Smiler’ ride suffered leg amputations and three others were also seriously injured when their carriage collided with a stationary carriage on the same track in June.
The Poole, Dorset-based company will face a charge under the Health and Safety at Work Act 1974.
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 there is sufficient evidence and that it is in the public interest to bring a prosecution."
Also on Thursday, Merlin reported broadly flat visitor numbers, a 2.3% rise in revenue to £1.3bn and a 2.1% decline in pre-tax underlying earnings to £402mln in the year to December 26.
Pre-tax profits rose 0.3% to £250mln. It increased its dividend by 4.8% to 6.5p per share. Shares in the group rose 10.7p to 445.4p.
Chief executive Nick Varney said: "2015 was a difficult year for Merlin following the accident at Alton Towers early in the summer season.
"The safety of our guests and employees must always come first and we have sought to learn every possible lesson to help ensure there is no repeat of what happened on June 2."