The Care Quality Commission (CQC) said it followed an incident at Melbury Lodge, Royal Hampshire County Hospital.
In December 2015 a patient sustained serious injuries during a fall from a low roof at the Winchester hospital run by Southern Health.
The CQC said the alleged offence by the trust was failing to provide safe care and treatment to a service user.
Melbury Lodge treats people with severe mental health problems.
The case is expected to be heard later in the year by Basingstoke Magistrates' Court.
Southern Health NHS Foundation Trust is to face prosecution over alleged failings at a mental health unit.