The filmmaker, who won the prestigious Palme d'Or at Cannes in 1998 for "Eternity and a Day", often spent summers with his family at the house in Mati, east of the capital.
"My husband's books, his letters from celebrities, all the texts that authors had dedicated to him" were destroyed in the fire, Phoebe Angelopoulou told local television.
She said the collection had also included texts and poems written by her late husband.
Angelopoulou managed to flee the flames, which struck on Monday evening, with her granddaughter, but the house was severely damaged.
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Angelopoulos pioneered Greece's "new wave" cinema following the fall of the country's military dictatorship in 1974.
His works include "Landscape in the Mist" and "The Dust of Time".
He was killed in a freak accident in January 2012 while filming "The Other Sea", a project to document the effects of Greece's debt crisis.
More than 80 people have died in Greece this week in the deadliest wildfire outbreak in Europe this century.