Merlin Attractions Operation Ltd based in Poole, Dorset, will appear at North Staffordshire Justice Centre, Newcastle-under-Lyme on April 22 2016 to face a charge under the Health and Safety at Work Act etc, 1974.
After last June's accident, two women had legs amputated after their carriage collided with a stationary carriage on the same track.
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."
Sixteen people were injured in the collision on a low section of the ride, which can reach speeds of up to 50mph.
The five seriously injured were Vicky Balch and Daniel Thorpe, from Buxton in Derbyshire, Leah Washington and Joe Pugh, from Barnsley, and Chandaben Chauhan, from Wednesbury. Miss Washington and Miss Balch each lost a leg as a result of their injuries.
A Merlin statement said: "We have cooperated fully with the Health and Safety Executive (HSE) throughout their investigation while continuing to support those who were injured in the accident.
"The company completed its own investigation and published the results in November, accepting responsibility for what happened. We have also kept the HSE fully informed of the subsequent actions that we have taken to ensure that something like this cannot happen again."
Merlin Attractions Operations Ltd is the company responsible for Alton Towers and under health and safety law is responsible for managing the risks created by the operation of the theme park's rides.
Merlin Entertainments has seen its annual profits edge up after the accident.
The group - which also owns attractions such as Legoland, Madame Tussauds and the London Eye - said it overcame a fall in revenues at its theme parks to post a pre-tax profit rise of 0.3% to £250 million in the year to December 26 compared with a year ago.
It said Alton Towers had a "significant" fall in visitor numbers after the accident on June 2 2015, which resulted in the 500-acre theme park in Staffordshire being shut down for four days.
Merlin Attractions Operations Ltd are alleged to have breached Section 3(1) of the Health and Safety at Work etc Act 1974, which states: "It shall be the duty of every employer to conduct his undertaking in such a way as to ensure, so far as is reasonably practicable, that persons not in his employment who may be affected thereby are not thereby exposed to risks to their health or safety."