Duxbury's departure follows the arrival of David Sullivan and David Gold as joint owners, along with Karren Brady, and given his close relationship with manager Gianfranco Zola, speculation will begin over the future of the Italian at Upton Park.
West Hams Gianfranco Zola confident Lucas Neill will sign new contractWest Ham to move for Inter Milan pairWest Ham United sold to CB Holdings with promise of player investmentSullivan insisted when he arrived that Zola would remain as manager, despite reports linking former Manchester City manager Mark Hughes with a move to East London.
Brady said: 'We thank Scott for his valued contribution and wish him every success in the future.'
Duxbury added: 'I wish Mr Sullivan, Mr Gold and Karren great success in driving this wonderful club forward and I know under their stewardship the club will prosper.'
Duxbury has presided over one of the most difficult periods in the history of the club, including the Carlos Tevez affair and the recent financial problems which led to the arrival of new owners.