Jones, Obama's green jobs "czar," was caught on tape, suggesting government's role in 2001 terror attacks, Washington Times reported on Sep 6.
Politicians had been calling for Jones to resign after it was revealed in recent days he signed a petition supporting 9/11 conspiracy theories.
In a resignation letter released by the White House early Sep 6, Mr Jones said he was the victim of a smear campaign.
He said, "On the eve of historic fights for health care and clean energy, opponents of reform have mounted a vicious smear campaign against me. They are using lies and distortions to distract and divide."
Jones said while he's been getting encouragement from both political parties to "stay and fight," he "cannot in good conscience ask my colleagues to expend precious time and energy defending or explaining my past."