Steve Carter (pictured above) who has been described as one of Hybels' heirs, wrote on his blog that he had made the decision some time ago following the church's handling of the allegations.
Hybels has been accused of sexual misconduct, with the latest claim being made in the New York Times that he indecently touched a former assistant.
While Hybels stood down from church ministry when the allegations first surfaced, he denied wrongdoing but apologised for being "unwise" and potentially misleading people.
Willow Creek has faced much criticism over its handling of the situation. Previous to the allegations being made public and internal investigation cleared him of any misconduct.
Ten women have now come forward with allegations.
Responding to the situation, Steve Carter wrote: "Since the first women came forward with their stories, I have been gravely concerned about our church's official response, and its ongoing approach to these painful issues.
"After many frank conversations with our elders, it became clear that there is a fundamental difference in judgment between what I believe is necessary for Willow Creek to move in a positive direction, and what they think is best.
"That is not to say that I am right and they are wrong. But I must follow the path that I believe God has laid out for me to live with integrity, and that path now diverges from Willow Creek.
"I offered my resignation many weeks ago, but I was requested to delay an announcement and continue with my duties until the leadership determined how to make the decision public. At this point, however, I cannot, in good conscience, appear before you as your Lead Teaching Pastor when my soul is so at odds with the institution."
Carter's resignation comes days before Willow Creek hosts the Global Leadership Summit where church leaders from across the world gather.
It'll be the first time the event isn't hosted by Bill Hybels.
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