The bottom line is that she cannot change a child's surname without your consent, so you can ask her to revert back to the surname on his birth certificate.
You can inform the school that his birth name should be used. The school are not permitted to allow the child to have a 'known as' name unless those with parental responsibility agree - which obviously you do not.
If the mother refuses to change it back, then your only option is court really, though before applying to court you are obliged to try mediation.
You would be applying for a prohibited steps order to prevent the mother allowing the child to be known as any other name than the one he has on his birth certificate. The application is made on form C100, current cost is £215. If you're on a low income/benefits you may be eligible for fee remission. All the forms and links you need are below:
Find a mediator here: www.familymediationcouncil.org.uk
C100 form: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/946762/c100-eng.pdf
EX160 form: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/952045/ex160-eng.pdf
E160A Notes: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/958038/ex160a-eng.pdf