The cuts are being made after Isle of Portland Aldridge Community Academy introduced "stage not age" principles, whereby children move classes when they are ready, rather than simply by age.
Principal Joss Hayes said the changes would provide "the very best education and opportunities".
The school said it hoped most redundancies would be voluntary.
It said the new structure would reflect a "schools within schools" model, each with separate heads and staff responsible for all aspects of a child's teaching and progression.
The new structure is due to be in place when the academy's new campus at Maritime House, Southwell, opens in September.
Governors have agreed to 21 posts being made redundant as part of the reorganisation, equating to 15 full time members of staff. Two are teaching or senior leadership roles, the remainder being teaching assistants and support staff posts.
A consultation with staff and trade unions over the changes began last year.
The academy, for four to 19-year-olds, replaced four of the island's schools when it opened in September 2012.
An academy school in Dorset is set to cut 15 jobs as part of a restructuring programme.