Prof Dame Glynis Breakwell earns £451,000 a year and is the highest paid vice-chancellor in the country.
Andrew Murrison, Conservative MP for South West Wiltshire, said university bosses were "looking increasingly like a self-serving cartel".
The former defence and Northern Ireland minister, has written to the university to resign as an ex-officio member.
"Universities really need to be asking whether the eye-watering sums some are dispensing to vice-chancellors are really necessary to attract what they represent as talent," he said.
"As a pack, they are looking increasingly like a self-serving cartel at a time of mounting student debt and wage restraint elsewhere in the public and quasi-public sectors.
"I cannot in all conscience continue to be associated with the governance of Bath University, in however titular a capacity, whilst current practice remains unchallenged."
Mr Murrison stood down from the Court of Bath University, a statutory body representing the interests of the university's internal and external stakeholders.
The South West Wiltshire MP also expressed concerns over pay to Hugh Brady the vice-chancellor of Bristol University, where Mr Murrison is an associated ex-officio member.
The resignation follows a debate in the House of Lords last month, in which former education minister Lord Adonis accused the University of Bath's remuneration committee of being "mired in controversy".
He said the "only example" the vice-chancellor was setting to her staff was "one of greed".
The Higher Education Funding Council for England watchdog is currently investigating whether the way pay is awarded is sufficiently transparent.
A university spokesman has said it is "committed to the highest standards of governance" and its "remuneration process" was "in line with practice at other universities"
University chiefs took home salary packages worth more than £250,000 on average last year, according to the University and College Union.
An MP has quit his role at the University of Bath in protest over the vice-chancellor's "eye-watering" pay.