Waddell, named Consumer Magazine Publisher of the Year at the 2006 Periodical Publishers Association Awards, has worked at the BBC for 14 years. He joined in 1992 ahead of the launch of Top Gear after three years on Haymarket's Autosport.
His new role has been created after the departure of the BBC Good Homes and Homes and Antiques publisher Brian Whittaker.
Marcus Arthur, the managing director of BBC Magazines London, said: "Adam has taken Top Gear from strength to strength, establishing a magazine that has become much more than just a niche motoring title. Of all the men's magazines, now only FHM has more male ABC1 readers. Adam is perfect for leading BBC Good Homes and Top Gear to even greater success."