The collection contains images from throughout the revered actor's career, including portraits from films such as Dracula (1958), The Wicker Man (1973) and The Lord Of The Rings trilogy.
Also included in the archive, donated by Sir Christopher's wife, Lady Gitte, are previously unseen on-set stills and contact sheets.
Sir Christopher, who was honoured with a BFI fellowship in 2013, died at the age of 93 in 2015.
Lady Gitte Lee said: "It was a great joy and an honour for my husband when he was awarded the BFI Fellowship in recognition for his lifelong contribution to the industry.
"I am therefore delighted that the BFI are helping to preserve the heritage of his legacy, by bringing Christopher's photographic archive into the BFI National Archive.
"I am immensely proud of my husband's achievements. One of Britain's best-loved actors, he was a man who entertained audiences worldwide for more than 60 years.
"It gives me great pleasure that his photos will be seen and appreciated for generations to come."
The Sir Christopher Lee Archive provides a "unique first-person account of an extraordinary and prolific career", the BFI said, with previously unseen annotated musings "revealing his crisp, dry humour".
The collection spans more than 60 years.
Nathalie Morris, senior curator of special collections at the BFI, said: "The albums are fascinating for being assembled by Lee himself, especially as they also include his occasional, wryly-observed, comments."
London-born Sir Christopher was known for playing villains throughout his storied career, perhaps most famously Dracula in the Hammer Horror films.
Other roles included Francisco Scaramanga in the James Bond film The Man With The Golden Gun (1974) and Saruman in The Lord of the Rings film trilogy (2001-2003).
Sir Christopher was knighted for services to drama and charity in 2009.