Actually, technically, she isn’t. The Head of the Church of England is officially, Jesus Christ (Henry VIII did style himself as Head, and so did his two immediate successors, but from the reign of Elizabeth I, this changed). The Queen is the Supreme Governor. But she does not set the policy of the Church. That is in the hands of the Archbishops and Bishops - in particular, the Lords Spiritual who are also part of the British government (they have seats in the House of Lords) - and the Synod.
All being the Supreme Governor really means is that the Archbishops and Bishops can’t assert their religious authority over her (ie, they can’t excommunicate her) in contrast to the way the Pope and occasionally other senior Catholic clergy used to do to Monarchs.