With a working title of “Royals Declassified”, the programme is based on declassified documents, including letters, diaries, eye-witness testimony and audio recordings.
The broadcaster said it will also feature interviews with royal insiders, historians and politicians.
The first episode will explore the Queen's relationships with former prime ministers, “including mounting tensions with Margaret Thatcher that threatened a constitutional crisis”.
Meanwhile, the second episode is set to “shed fresh light on the tensions she's experienced between the demands of her family and her role as monarch”.
Channel 4 said the final programme will “explores how a spy passing information to the Soviets was able to work for so many years in Buckingham Palace”.
Anthony Blunt, who was the Queen’s art adviser, was exposed as a Russian spy in 1979, but had privately confessed to the Soviet connection in 1964 when he was confronted by British authorities.
The Queen stripped him of the knighthood he had been awarded early in her reign after he was exposed. Blunt’s story was also covered in season three of Netflix’s The Crown and he was portrayed by actor Samuel West.
Speaking of the upcoming documentary, Shaminder Nahal, Channel 4 commissioning editor, specialist factual, said: “From the Queen's relationships with her prime ministers, to the extraordinary story of the spy in the palace and some of the Queen's family secrets – this series brings many intriguing aspects of the history of the Crown to life in primary colour – with wit, verve and fascinating detail.”
Dan Chambers, creative director of producers Blink Films, added: “What makes these films so compelling is the new evidence we've uncovered both from declassified documents and from contributors.”
No release date for the documentary has yet been shared.