Thomas was GM of the Phillies from June 1988 to December 1997 and also worked for the St. Louis Cardinals from 1970-88.
Thomas was a special assistant and an assistant GM to Duquette with the Red Sox, and was a pro scout for the Milwaukee Brewers from 2004-06.
Baltimore also said Sunday it had hired Fred Ferreira as executive director of international recruiting. A former executive with the New York Yankees, Cincinnati Reds, Montreal Expos and Florida Marlins, Ferreira signed Vladimir Guerrero, Bernie Williams and Orlando Cabrera.
Duquette was hired last month as the Orioles' executive vice president of baseball operations.