In a statement on Tuesday Bolton, who joined the organisation in 2014, did not give a reason for her decision.
Last week two board members, deputy chair Heather Hancock and audit committee chair Martin Stewart also stood down amid reports of differences between the board and London 2017 chairman Ed Warner, who is also chairman of UK Athletics.
"I'm incredibly proud of the work that has been completed in achieving the early milestones that lay the foundations for the event's success," Bolton said.
The world championships, the flagship event for the embattled International Association of Athletics Federations (IAAF) are being held in London for the first time.
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(Reporting by Martyn Herman; Editing by Dominic Evans)
